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2AFI
Asym. Unit
Info
Asym.Unit (994 KB)
Biol.Unit 1 (497 KB)
Biol.Unit 2 (495 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF MGADP BOUND AV2-AV1 COMPLEX
Authors
:
F. A. Tezcan, J. T. Kaiser, D. Mustafi, M. Y. Walton, J. B. Howard, D. C. Rees
Date
:
25 Jul 05 (Deposition) - 06 Sep 05 (Release) - 05 May 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Biol. Unit 2: I,J,K,L,M,N,O,P (1x)
Keywords
:
Nitrogen Fixation, Iron-Sulfur, Metal-Binding, Molybdenum, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. A. Tezcan, J. T. Kaiser, D. Mustafi, M. Y. Walton, J. B. Howard, D. C. Rees
Nitrogenase Complexes: Multiple Docking Sites For A Nucleotide Switch Protein
Science V. 309 1377 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(7, 36)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
1c: ADENOSINE-5'-DIPHOSPHATE (ADPc)
1d: ADENOSINE-5'-DIPHOSPHATE (ADPd)
1e: ADENOSINE-5'-DIPHOSPHATE (ADPe)
1f: ADENOSINE-5'-DIPHOSPHATE (ADPf)
1g: ADENOSINE-5'-DIPHOSPHATE (ADPg)
1h: ADENOSINE-5'-DIPHOSPHATE (ADPh)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
2c: CALCIUM ION (CAc)
2d: CALCIUM ION (CAd)
3a: FE(7)-MO-S(9)-N CLUSTER (CFNa)
3b: FE(7)-MO-S(9)-N CLUSTER (CFNb)
3c: FE(7)-MO-S(9)-N CLUSTER (CFNc)
3d: FE(7)-MO-S(9)-N CLUSTER (CFNd)
4a: FE(8)-S(7) CLUSTER (CLFa)
4b: FE(8)-S(7) CLUSTER (CLFb)
4c: FE(8)-S(7) CLUSTER (CLFc)
4d: FE(8)-S(7) CLUSTER (CLFd)
5a: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAa)
5b: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAb)
5c: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAc)
5d: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAd)
6a: MAGNESIUM ION (MGa)
6b: MAGNESIUM ION (MGb)
6c: MAGNESIUM ION (MGc)
6d: MAGNESIUM ION (MGd)
6e: MAGNESIUM ION (MGe)
6f: MAGNESIUM ION (MGf)
6g: MAGNESIUM ION (MGg)
6h: MAGNESIUM ION (MGh)
7a: IRON/SULFUR CLUSTER (SF4a)
7b: IRON/SULFUR CLUSTER (SF4b)
7c: IRON/SULFUR CLUSTER (SF4c)
7d: IRON/SULFUR CLUSTER (SF4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
8
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
CA
4
Ligand/Ion
CALCIUM ION
3
CFN
4
Ligand/Ion
FE(7)-MO-S(9)-N CLUSTER
4
CLF
4
Ligand/Ion
FE(8)-S(7) CLUSTER
5
HCA
4
Ligand/Ion
3-HYDROXY-3-CARBOXY-ADIPIC ACID
6
MG
8
Ligand/Ion
MAGNESIUM ION
7
SF4
4
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(36, 36)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG B:108 , GLU B:109 , HOH B:9000 , ASP D:353 , ASP D:357 , HOH D:9001
BINDING SITE FOR RESIDUE CA B 2492
02
AC2
SOFTWARE
ASP B:353 , ASP B:357 , HOH B:9003 , ARG D:108 , GLU D:109 , HOH D:9002
BINDING SITE FOR RESIDUE CA B 4492
03
AC3
SOFTWARE
SER E:16 , ASP E:43 , ADP E:1292
BINDING SITE FOR RESIDUE MG E 1291
04
AC4
SOFTWARE
SER F:16 , ASP F:43 , ADP F:2292
BINDING SITE FOR RESIDUE MG F 2291
05
AC5
SOFTWARE
SER G:16 , ASP G:39 , ASP G:43 , ASP G:125 , ADP G:3292
BINDING SITE FOR RESIDUE MG G 3291
06
AC6
SOFTWARE
SER H:16 , ADP H:4292
BINDING SITE FOR RESIDUE MG H 4291
07
AC7
SOFTWARE
ARG J:108 , GLU J:109 , HOH J:9004 , ASP L:353 , ASP L:357 , HOH L:9005
BINDING SITE FOR RESIDUE CA L 6492
08
AC8
SOFTWARE
ASP J:353 , ASP J:357 , HOH J:9007 , ARG L:108 , GLU L:109 , HOH L:9006
BINDING SITE FOR RESIDUE CA J 8492
09
AC9
SOFTWARE
SER M:16 , ADP M:5292
BINDING SITE FOR RESIDUE MG M 5291
10
BC1
SOFTWARE
ASP N:43 , ADP N:6292
BINDING SITE FOR RESIDUE MG N 6291
11
BC2
SOFTWARE
SER O:16 , ASP O:43 , ADP O:7292
BINDING SITE FOR RESIDUE MG O 7291
12
BC3
SOFTWARE
SER P:16 , ASP P:125 , ADP P:8292
BINDING SITE FOR RESIDUE MG P 8291
13
BC4
SOFTWARE
ALA A:65 , GLN A:191 , GLY A:424 , ILE A:425 , HIS A:442 , CFN A:496
BINDING SITE FOR RESIDUE HCA A 494
14
BC5
SOFTWARE
VAL A:70 , ARG A:96 , HIS A:195 , TYR A:229 , CYS A:275 , GLY A:357 , LEU A:358 , ARG A:359 , PHE A:381 , HIS A:442 , HCA A:494
BINDING SITE FOR RESIDUE CFN A 496
15
BC6
SOFTWARE
CYS A:62 , PRO A:85 , CYS A:88 , TYR A:91 , CYS A:154 , GLY A:185 , CYS B:70 , SER B:92 , GLY B:94 , CYS B:95 , TYR B:98 , CYS B:153 , SER B:188
BINDING SITE FOR RESIDUE CLF B 1498
16
BC7
SOFTWARE
ALA C:65 , GLN C:191 , GLY C:424 , ILE C:425 , HIS C:442 , CFN C:496
BINDING SITE FOR RESIDUE HCA C 494
17
BC8
SOFTWARE
ARG C:96 , HIS C:195 , TYR C:229 , CYS C:275 , ILE C:355 , GLY C:357 , LEU C:358 , ARG C:359 , PHE C:381 , HIS C:442 , HCA C:494
BINDING SITE FOR RESIDUE CFN C 496
18
BC9
SOFTWARE
CYS C:62 , PRO C:85 , CYS C:88 , TYR C:91 , CYS C:154 , GLY C:185 , CYS D:70 , SER D:92 , CYS D:95 , TYR D:98 , THR D:152 , CYS D:153 , SER D:188
BINDING SITE FOR RESIDUE CLF D 3498
19
CC1
SOFTWARE
CYS E:97 , CYS E:132 , CYS F:97 , ALA F:98 , GLY F:99 , CYS F:132
BINDING SITE FOR RESIDUE SF4 F 1290
20
CC2
SOFTWARE
LYS E:10 , GLY E:11 , GLY E:12 , ILE E:13 , GLY E:14 , LYS E:15 , SER E:16 , THR E:17 , PRO E:212 , ASP E:214 , VAL E:217 , GLN E:218 , GLU E:221 , MG E:1291 , MET F:156
BINDING SITE FOR RESIDUE ADP E 1292
21
CC3
SOFTWARE
MET E:156 , GLY F:11 , GLY F:12 , ILE F:13 , GLY F:14 , LYS F:15 , SER F:16 , THR F:17 , LYS F:41 , ASN F:185 , VAL F:211 , PRO F:212 , ARG F:213 , ASP F:214 , VAL F:217 , TYR F:240 , MG F:2291
BINDING SITE FOR RESIDUE ADP F 2292
22
CC4
SOFTWARE
ALA G:98 , GLY G:99 , CYS G:132 , GLY G:134 , CYS H:97 , CYS H:132 , PHE H:135
BINDING SITE FOR RESIDUE SF4 G 3290
23
CC5
SOFTWARE
LYS G:10 , GLY G:11 , GLY G:12 , ILE G:13 , GLY G:14 , LYS G:15 , SER G:16 , THR G:17 , ASN G:185 , VAL G:211 , PRO G:212 , ARG G:213 , ASP G:214 , GLU G:221 , MG G:3291
BINDING SITE FOR RESIDUE ADP G 3292
24
CC6
SOFTWARE
GLY H:12 , ILE H:13 , GLY H:14 , LYS H:15 , SER H:16 , THR H:17 , MG H:4291
BINDING SITE FOR RESIDUE ADP H 4292
25
CC7
SOFTWARE
ALA I:65 , GLN I:191 , GLY I:424 , ILE I:425 , HIS I:442 , CFN I:496
BINDING SITE FOR RESIDUE HCA I 494
26
CC8
SOFTWARE
VAL I:70 , ARG I:96 , HIS I:195 , TYR I:229 , CYS I:275 , ILE I:355 , GLY I:357 , LEU I:358 , ARG I:359 , PHE I:381 , HIS I:442 , HCA I:494
BINDING SITE FOR RESIDUE CFN I 496
27
CC9
SOFTWARE
CYS I:62 , PRO I:85 , CYS I:88 , TYR I:91 , CYS I:154 , GLY I:185 , CYS J:70 , SER J:92 , GLY J:94 , CYS J:95 , TYR J:98 , CYS J:153 , SER J:188
BINDING SITE FOR RESIDUE CLF J 5498
28
DC1
SOFTWARE
ALA K:65 , GLN K:191 , GLY K:424 , ILE K:425 , HIS K:442 , CFN K:496
BINDING SITE FOR RESIDUE HCA K 494
29
DC2
SOFTWARE
VAL K:70 , ARG K:96 , HIS K:195 , TYR K:229 , CYS K:275 , ILE K:355 , GLY K:357 , LEU K:358 , ARG K:359 , PHE K:381 , HIS K:442 , HCA K:494
BINDING SITE FOR RESIDUE CFN K 496
30
DC3
SOFTWARE
CYS K:62 , PRO K:85 , CYS K:88 , TYR K:91 , CYS K:154 , GLY K:185 , CYS L:70 , SER L:92 , GLY L:94 , CYS L:95 , TYR L:98 , THR L:152 , CYS L:153 , SER L:188
BINDING SITE FOR RESIDUE CLF L 7498
31
DC4
SOFTWARE
CYS M:97 , ALA M:98 , CYS M:132 , CYS N:97 , CYS N:132
BINDING SITE FOR RESIDUE SF4 N 5290
32
DC5
SOFTWARE
GLY M:12 , GLY M:14 , LYS M:15 , SER M:16 , THR M:17 , ASN M:185 , VAL M:211 , PRO M:212 , ARG M:213 , ASP M:214 , TYR M:240 , MG M:5291
BINDING SITE FOR RESIDUE ADP M 5292
33
DC6
SOFTWARE
GLY N:12 , GLY N:14 , LYS N:15 , SER N:16 , THR N:17 , MG N:6291
BINDING SITE FOR RESIDUE ADP N 6292
34
DC7
SOFTWARE
CYS O:97 , ALA O:98 , CYS O:132 , CYS P:97 , ALA P:98 , CYS P:132 , GLY P:134 , PHE P:135
BINDING SITE FOR RESIDUE SF4 P 7290
35
DC8
SOFTWARE
LYS O:10 , GLY O:11 , GLY O:12 , ILE O:13 , GLY O:14 , LYS O:15 , SER O:16 , THR O:17 , ASP O:43 , ASN O:185 , ARG O:213 , ASP O:214 , TYR O:240 , MG O:7291
BINDING SITE FOR RESIDUE ADP O 7292
36
DC9
SOFTWARE
MET O:156 , GLY P:12 , ILE P:13 , GLY P:14 , LYS P:15 , SER P:16 , THR P:17 , PRO P:212 , ASP P:214 , MG P:8291
BINDING SITE FOR RESIDUE ADP P 8292
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(5, 37)
Info
All PROSITE Patterns/Profiles
1: NIFH_FRXC_3 (E:2-271,F:2-274,G:2-263,H:2-270,O:...)
2: NITROGENASE_1_1 (A:81-88,C:81-88,I:81-88,K:81-88,B:...)
3: NIFH_FRXC_1 (E:87-99,F:87-99,G:87-99,H:87-99,M:...)
4: NIFH_FRXC_2 (E:125-138,F:125-138,G:125-138,H:12...)
5: NITROGENASE_1_2 (B:151-165,D:151-165,J:151-165,L:15...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NIFH_FRXC_3
PS51026
NIFH_FRXC family profile.
NIFH1_AZOVI
3-275
5
E:2-271
F:2-274
G:2-263
H:2-270
O:2-263
2
NITROGENASE_1_1
PS00699
Nitrogenases component 1 alpha and beta subunits signature 1.
NIFD_AZOVI
81-88
4
A:81-88
C:81-88
I:81-88
K:81-88
NIFK_AZOVI
88-95
4
B:88-95
D:88-95
J:88-95
L:88-95
3
NIFH_FRXC_1
PS00746
NifH/frxC family signature 1.
NIFH1_AZOVI
88-100
8
E:87-99
F:87-99
G:87-99
H:87-99
M:87-99
N:87-99
O:87-99
P:87-99
4
NIFH_FRXC_2
PS00692
NifH/frxC family signature 2.
NIFH1_AZOVI
126-139
8
E:125-138
F:125-138
G:125-138
H:125-138
M:125-138
N:125-138
O:125-138
P:125-138
5
NITROGENASE_1_2
PS00090
Nitrogenases component 1 alpha and beta subunits signature 2.
NIFK_AZOVI
151-165
4
B:151-165
D:151-165
J:151-165
L:151-165
NIFD_AZOVI
152-166
4
A:152-166
C:152-166
I:152-166
K:152-166
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 16)
Info
All SCOP Domains
1a: SCOP_d2afia_ (A:)
1b: SCOP_d2afib_ (B:)
1c: SCOP_d2afic_ (C:)
1d: SCOP_d2afid_ (D:)
1e: SCOP_d2afii_ (I:)
1f: SCOP_d2afij_ (J:)
1g: SCOP_d2afik_ (K:)
1h: SCOP_d2afil_ (L:)
2a: SCOP_d2afie_ (E:)
2b: SCOP_d2afif_ (F:)
2c: SCOP_d2afig_ (G:)
2d: SCOP_d2afih_ (H:)
2e: SCOP_d2afim_ (M:)
2f: SCOP_d2afin_ (N:)
2g: SCOP_d2afio_ (O:)
2h: SCOP_d2afip_ (P:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Chelatase-like
(149)
Superfamily
:
Helical backbone metal receptor
(102)
Family
:
Nitrogenase iron-molybdenum protein
(41)
Protein domain
:
automated matches
(6)
Azotobacter vinelandii [TaxId: 354]
(6)
1a
d2afia_
A:
1b
d2afib_
B:
1c
d2afic_
C:
1d
d2afid_
D:
1e
d2afii_
I:
1f
d2afij_
J:
1g
d2afik_
K:
1h
d2afil_
L:
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
Nitrogenase iron protein-like
(152)
Protein domain
:
Nitrogenase iron protein
(21)
Azotobacter vinelandii [TaxId: 354]
(20)
2a
d2afie_
E:
2b
d2afif_
F:
2c
d2afig_
G:
2d
d2afih_
H:
2e
d2afim_
M:
2f
d2afin_
N:
2g
d2afio_
O:
2h
d2afip_
P:
[
close SCOP info
]
CATH Domains
(3, 36)
Info
all CATH domains
1a: CATH_2afiA02 (A:63-205)
1b: CATH_2afiB02 (B:216-320)
1c: CATH_2afiD02 (D:216-320)
1d: CATH_2afiJ02 (J:216-320)
1e: CATH_2afiL02 (L:216-320)
1f: CATH_2afiA01 (A:5-62,A:345-479)
1g: CATH_2afiC01 (C:5-62,C:345-479)
1h: CATH_2afiI01 (I:5-62,I:345-479)
1i: CATH_2afiK01 (K:5-62,K:345-479)
1j: CATH_2afiC02 (C:63-205)
1k: CATH_2afiI02 (I:63-205)
1l: CATH_2afiK02 (K:63-205)
1m: CATH_2afiB01 (B:70-215)
1n: CATH_2afiD01 (D:70-215)
1o: CATH_2afiJ01 (J:70-215)
1p: CATH_2afiL01 (L:70-215)
1q: CATH_2afiA03 (A:206-320)
1r: CATH_2afiC03 (C:206-320)
1s: CATH_2afiI03 (I:206-320)
1t: CATH_2afiK03 (K:206-320)
1u: CATH_2afiB04 (B:365-470)
1v: CATH_2afiD04 (D:365-470)
1w: CATH_2afiJ04 (J:365-470)
1x: CATH_2afiL04 (L:365-470)
2a: CATH_2afiO00 (O:2-263)
2b: CATH_2afiG00 (G:1-263)
2c: CATH_2afiP00 (P:6-272)
2d: CATH_2afiM00 (M:4-271)
2e: CATH_2afiH00 (H:2-270)
2f: CATH_2afiN00 (N:4-273)
2g: CATH_2afiE00 (E:1-271)
2h: CATH_2afiF00 (F:1-275)
3a: CATH_2afiB03 (B:321-364,B:485-523)
3b: CATH_2afiD03 (D:321-364,D:485-523)
3c: CATH_2afiJ03 (J:321-364,J:485-523)
3d: CATH_2afiL03 (L:321-364,L:485-523)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Nitrogenase molybdenum iron protein domain
(45)
Azotobacter vinelandii. Organism_taxid: 354. Azotobacter vinelandii. Organism_taxid: 354.
(8)
1a
2afiA02
A:63-205
1b
2afiB02
B:216-320
1c
2afiD02
D:216-320
1d
2afiJ02
J:216-320
1e
2afiL02
L:216-320
1f
2afiA01
A:5-62,A:345-479
1g
2afiC01
C:5-62,C:345-479
1h
2afiI01
I:5-62,I:345-479
1i
2afiK01
K:5-62,K:345-479
1j
2afiC02
C:63-205
1k
2afiI02
I:63-205
1l
2afiK02
K:63-205
1m
2afiB01
B:70-215
1n
2afiD01
D:70-215
1o
2afiJ01
J:70-215
1p
2afiL01
L:70-215
1q
2afiA03
A:206-320
1r
2afiC03
C:206-320
1s
2afiI03
I:206-320
1t
2afiK03
K:206-320
1u
2afiB04
B:365-470
1v
2afiD04
D:365-470
1w
2afiJ04
J:365-470
1x
2afiL04
L:365-470
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Azotobacter vinelandii. Organism_taxid: 354. Azotobacter vinelandii. Organism_taxid: 354.
(8)
2a
2afiO00
O:2-263
2b
2afiG00
G:1-263
2c
2afiP00
P:6-272
2d
2afiM00
M:4-271
2e
2afiH00
H:2-270
2f
2afiN00
N:4-273
2g
2afiE00
E:1-271
2h
2afiF00
F:1-275
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Nitrogenase Molybdenum-iron Protein, subunit B; domain 4
(19)
Homologous Superfamily
:
Nitrogenase Molybdenum-iron Protein, subunit B, domain 4
(19)
Azotobacter vinelandii. Organism_taxid: 354. Azotobacter vinelandii. Organism_taxid: 354.
(8)
3a
2afiB03
B:321-364,B:485-523
3b
2afiD03
D:321-364,D:485-523
3c
2afiJ03
J:321-364,J:485-523
3d
2afiL03
L:321-364,L:485-523
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