PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
4WZA
Asym. Unit
Info
Asym.Unit (1.0 MB)
Biol.Unit 1, α-C (1.0 MB)
Biol.Unit 1 (1.0 MB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ASYMMETRIC NUCLEOTIDE BINDING IN THE NITROGENASE COMPLEX
Authors
:
F. A. Tezcan, J. T. Kaiser, J. B. Howard, D. C. Rees
Date
:
19 Nov 14 (Deposition) - 31 Dec 14 (Release) - 28 Jan 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D,E,F,G,H (1x)
Keywords
:
Nitrogenase, Nucleotide Binding, Asymetry, Complex, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. A. Tezcan, J. T. Kaiser, J. B. Howard, D. C. Rees
Structural Evidence For Asymmetrical Nucleotide Interaction In Nitrogenase.
J. Am. Chem. Soc. V. 137 146 2015
[
close entry info
]
Hetero Components
(8, 18)
Info
All Hetero Components
1a: PHOSPHOMETHYLPHOSPHONIC ACID ADENY... (ACPa)
1b: PHOSPHOMETHYLPHOSPHONIC ACID ADENY... (ACPb)
2a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
2b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
3a: FE(8)-S(7) CLUSTER (CLFa)
3b: FE(8)-S(7) CLUSTER (CLFb)
4a: FE (III) ION (FEa)
4b: FE (III) ION (FEb)
5a: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAa)
5b: 3-HYDROXY-3-CARBOXY-ADIPIC ACID (HCAb)
6a: IRON-SULFUR-MOLYBDENUM CLUSTER WIT... (ICSa)
6b: IRON-SULFUR-MOLYBDENUM CLUSTER WIT... (ICSb)
7a: MAGNESIUM ION (MGa)
7b: MAGNESIUM ION (MGb)
7c: MAGNESIUM ION (MGc)
7d: MAGNESIUM ION (MGd)
8a: IRON/SULFUR CLUSTER (SF4a)
8b: IRON/SULFUR CLUSTER (SF4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACP
2
Ligand/Ion
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
2
ADP
2
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
3
CLF
2
Ligand/Ion
FE(8)-S(7) CLUSTER
4
FE
2
Ligand/Ion
FE (III) ION
5
HCA
2
Ligand/Ion
3-HYDROXY-3-CARBOXY-ADIPIC ACID
6
ICS
2
Ligand/Ion
IRON-SULFUR-MOLYBDENUM CLUSTER WITH INTERSTITIAL CARBON
7
MG
4
Ligand/Ion
MAGNESIUM ION
8
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(18, 18)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ALA A:65 , GLN A:191 , GLY A:424 , ILE A:425 , HIS A:442 , ICS A:1496 , HOH A:1507 , HOH A:1519 , HOH A:1532 , HOH A:1572 , HOH A:1582 , HOH A:1587 , HOH A:1588 , HOH A:1778 , HOH B:1528 , HOH B:1653
binding site for residue HCA A 1494
02
AC2
SOFTWARE
VAL A:70 , ARG A:96 , HIS A:195 , TYR A:229 , CYS A:275 , GLY A:356 , GLY A:357 , LEU A:358 , ARG A:359 , PHE A:381 , HIS A:442 , HCA A:1494
binding site for residue ICS A 1496
03
AC3
SOFTWARE
CYS A:62 , TYR A:64 , PRO A:85 , GLY A:87 , CYS A:88 , TYR A:91 , CYS A:154 , GLY A:185 , CYS B:70 , SER B:92 , CYS B:95 , TYR B:98 , CYS B:153 , SER B:188
binding site for residue CLF A 1498
04
AC4
SOFTWARE
ARG B:108 , GLU B:109 , HOH B:1629 , ASP D:353 , ASP D:357 , HOH D:1970
binding site for residue FE B 1492
05
AC5
SOFTWARE
ALA C:65 , GLN C:191 , GLY C:424 , ILE C:425 , HIS C:442 , ICS C:1496 , HOH C:1522 , HOH C:1530 , HOH C:1562 , HOH C:1591 , HOH C:1594 , HOH C:1595 , HOH C:1605 , HOH D:1560 , HOH D:1617 , HOH D:1619
binding site for residue HCA C 1494
06
AC6
SOFTWARE
VAL C:70 , ARG C:96 , HIS C:195 , TYR C:229 , CYS C:275 , GLY C:356 , GLY C:357 , LEU C:358 , ARG C:359 , PHE C:381 , HIS C:442 , HCA C:1494
binding site for residue ICS C 1496
07
AC7
SOFTWARE
CYS C:62 , TYR C:64 , PRO C:85 , GLY C:87 , CYS C:88 , TYR C:91 , CYS C:154 , GLY C:185 , CYS D:70 , SER D:92 , CYS D:95 , TYR D:98 , CYS D:153 , SER D:188
binding site for residue CLF C 1498
08
AC8
SOFTWARE
ASP B:353 , ASP B:357 , HOH B:1618 , ARG D:108 , GLU D:109 , HOH D:1935
binding site for residue FE D 1492
09
AC9
SOFTWARE
LEU A:158 , VAL B:157 , CYS E:97 , GLY E:99 , CYS E:132 , CYS F:97 , ALA F:98 , GLY F:99 , CYS F:132
binding site for residue SF4 E 1290
10
AD1
SOFTWARE
SER E:16 , ADP E:1292 , HOH E:1317 , HOH E:1318 , HOH E:1319 , HOH E:1320
binding site for residue MG E 1291
11
AD2
SOFTWARE
LYS E:10 , GLY E:12 , ILE E:13 , GLY E:14 , LYS E:15 , SER E:16 , THR E:17 , ASN E:185 , VAL E:211 , PRO E:212 , ARG E:213 , ASP E:214 , VAL E:217 , GLU E:221 , GLN E:236 , MG E:1291 , HOH E:1319 , HOH E:1320 , MET F:156
binding site for residue ADP E 1292
12
AD3
SOFTWARE
SER F:16 , ACP F:1292 , HOH F:1310 , HOH F:1311 , HOH F:1312
binding site for residue MG F 1291
13
AD4
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 , ASP F:39 , LYS F:41 , GLY F:128 , ASN F:185 , PRO F:212 , ARG F:213 , ASP F:214 , VAL F:217 , GLN F:218 , GLU F:221 , GLN F:236 , MG F:1291 , HOH F:1311 , HOH F:1312 , HOH F:1382
binding site for residue ACP F 1292
14
AD5
SOFTWARE
LEU C:158 , VAL D:157 , CYS G:97 , GLY G:99 , CYS G:132 , CYS H:97 , GLY H:99 , CYS H:132
binding site for residue SF4 G 1290
15
AD6
SOFTWARE
SER G:16 , ASP G:39 , ADP G:1292 , HOH G:1318 , HOH G:1319 , HOH G:1320 , HOH G:1321
binding site for residue MG G 1291
16
AD7
SOFTWARE
LYS G:10 , GLY G:12 , ILE G:13 , GLY G:14 , LYS G:15 , SER G:16 , THR G:17 , ASN G:185 , PRO G:212 , ARG G:213 , ASP G:214 , VAL G:217 , GLN G:218 , GLU G:221 , GLN G:236 , MG G:1291 , HOH G:1320 , HOH G:1321 , HOH G:1371
binding site for residue ADP G 1292
17
AD8
SOFTWARE
SER H:16 , ACP H:1292 , HOH H:1315 , HOH H:1316 , HOH H:1317
binding site for residue MG H 1291
18
AD9
SOFTWARE
LYS G:10 , MET G:156 , HOH G:1377 , GLY H:11 , GLY H:12 , ILE H:13 , GLY H:14 , LYS H:15 , SER H:16 , THR H:17 , ASP H:39 , LYS H:41 , GLY H:128 , ASN H:185 , PRO H:212 , ARG H:213 , ASP H:214 , VAL H:217 , GLN H:218 , GLU H:221 , GLN H:236 , MG H:1291 , HOH H:1316 , HOH H:1317 , HOH H:1392
binding site for residue ACP H 1292
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (1.0 MB)
Header - Asym.Unit
Biol.Unit 1 (1.0 MB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
4WZA
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help