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1OQU
Asym. Unit
Info
Asym.Unit (222 KB)
Biol.Unit 1 (108 KB)
Biol.Unit 2 (111 KB)
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(1)
Title
:
A PROTEIN COORDINATED TRI-NUCLEAR FE COMPLEX FORMED DURING SOAKING OF CRYSTALS OF THE RIBONUCLEOTIDE REDUCTASE R2F PROTEIN FROM CORYNEBACTERIUM AMMONIAGENES
Authors
:
M. Hogbom, P. Nordlund
Date
:
11 Mar 03 (Deposition) - 20 Apr 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Mineralization, Ferritin, Tri-Iron, Glutamate, Metal Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Hogbom, P. Nordlund
A Protein Carboxylate Coordinated Oxo-Centered Tri-Nuclear Iron Complex With Possible Implications For Ferritin Mineralization
Febs Lett. V. 567 179 2004
(for further references see the
PDB file header
)
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Hetero Components
(3, 24)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
2a: FE (III) ION (FEa)
2b: FE (III) ION (FEb)
2c: FE (III) ION (FEc)
2d: FE (III) ION (FEd)
2e: FE (III) ION (FEe)
2f: FE (III) ION (FEf)
2g: FE (III) ION (FEg)
2h: FE (III) ION (FEh)
2i: FE (III) ION (FEi)
2j: FE (III) ION (FEj)
2k: FE (III) ION (FEk)
2l: FE (III) ION (FEl)
2m: FE (III) ION (FEm)
2n: FE (III) ION (FEn)
2o: FE (III) ION (FEo)
2p: FE (III) ION (FEp)
2q: FE (III) ION (FEq)
2r: FE (III) ION (FEr)
2s: FE (III) ION (FEs)
2t: FE (III) ION (FEt)
3a: OXYGEN MOLECULE (OXYa)
3b: OXYGEN MOLECULE (OXYb)
3c: OXYGEN MOLECULE (OXYc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
1
Ligand/Ion
ACETATE ION
2
FE
20
Ligand/Ion
FE (III) ION
3
OXY
3
Ligand/Ion
OXYGEN MOLECULE
[
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Sites
(24, 24)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:77 , GLU A:108 , HIS A:111 , PHE A:172 , GLU A:202
BINDING SITE FOR RESIDUE FE A 1001
02
AC2
SOFTWARE
GLU A:108 , GLU A:168 , GLU A:202 , HIS A:205
BINDING SITE FOR RESIDUE FE A 1002
03
AC3
SOFTWARE
ASP B:77 , GLU B:108 , HIS B:111 , GLU B:202 , FE B:1004
BINDING SITE FOR RESIDUE FE B 1003
04
AC4
SOFTWARE
GLU B:108 , GLU B:168 , GLU B:202 , HIS B:205 , FE B:1003
BINDING SITE FOR RESIDUE FE B 1004
05
AC5
SOFTWARE
ASP C:77 , GLU C:108 , HIS C:111 , GLU C:202
BINDING SITE FOR RESIDUE FE C 1001
06
AC6
SOFTWARE
GLU C:108 , GLU C:168 , GLU C:202 , HIS C:205
BINDING SITE FOR RESIDUE FE C 1002
07
AC7
SOFTWARE
ASP D:77 , GLU D:108 , HIS D:111 , PHE D:172 , GLU D:202
BINDING SITE FOR RESIDUE FE D 1003
08
AC8
SOFTWARE
GLU D:108 , GLU D:168 , GLU D:202 , HIS D:205
BINDING SITE FOR RESIDUE FE D 1004
09
AC9
SOFTWARE
GLU A:245 , GLU A:248 , FE A:2002 , FE A:2003 , OXY A:2004 , HOH A:2063 , HOH A:2200
BINDING SITE FOR RESIDUE FE A 2001
10
BC1
SOFTWARE
GLU A:248 , FE A:2001 , FE A:2003 , OXY A:2004 , HOH A:2121 , HOH A:2192 , HOH A:2201
BINDING SITE FOR RESIDUE FE A 2002
11
BC2
SOFTWARE
GLU A:245 , FE A:2001 , FE A:2002 , OXY A:2004 , HOH A:2063 , HOH A:2201
BINDING SITE FOR RESIDUE FE A 2003
12
BC3
SOFTWARE
GLU B:248 , FE B:1006 , FE B:1007
BINDING SITE FOR RESIDUE FE B 1005
13
BC4
SOFTWARE
GLU B:248 , FE B:1005
BINDING SITE FOR RESIDUE FE B 1006
14
BC5
SOFTWARE
FE B:1005
BINDING SITE FOR RESIDUE FE B 1007
15
BC6
SOFTWARE
GLU C:245 , ASP C:324 , ASP C:326 , ASP C:328 , FE C:1009 , FE C:1010 , OXY C:1012 , HOH C:1214
BINDING SITE FOR RESIDUE FE C 1008
16
BC7
SOFTWARE
GLU C:248 , ASP C:326 , ASP C:328 , FE C:1008 , FE C:1010 , ACT C:1011 , OXY C:1012 , HOH C:1154
BINDING SITE FOR RESIDUE FE C 1009
17
BC8
SOFTWARE
GLU C:245 , GLU C:248 , ASP C:324 , FE C:1008 , FE C:1009 , ACT C:1011 , OXY C:1012 , HOH C:1188
BINDING SITE FOR RESIDUE FE C 1010
18
BC9
SOFTWARE
GLU D:248 , FE D:1014 , OXY D:1015 , HOH D:1033 , HOH D:1106 , HOH D:1127
BINDING SITE FOR RESIDUE FE D 1012
19
CC1
SOFTWARE
GLU D:245 , GLU D:248 , OXY D:1015 , HOH D:1033
BINDING SITE FOR RESIDUE FE D 1013
20
CC2
SOFTWARE
GLU D:245 , FE D:1012 , OXY D:1015 , HOH D:1127 , HOH D:1171
BINDING SITE FOR RESIDUE FE D 1014
21
CC3
SOFTWARE
GLU C:248 , ASP C:324 , ASP C:326 , FE C:1009 , FE C:1010 , OXY C:1012 , HOH C:1154 , HOH C:1163 , HOH C:1188
BINDING SITE FOR RESIDUE ACT C 1011
22
CC4
SOFTWARE
GLU A:245 , GLU A:248 , FE A:2001 , FE A:2002 , FE A:2003 , HOH A:2063 , HOH A:2121 , HOH A:2201
BINDING SITE FOR RESIDUE OXY A 2004
23
CC5
SOFTWARE
GLU C:245 , GLU C:248 , ASP C:324 , ASP C:326 , ASP C:328 , FE C:1008 , FE C:1009 , FE C:1010 , ACT C:1011
BINDING SITE FOR RESIDUE OXY C 1012
24
CC6
SOFTWARE
GLU D:245 , GLU D:248 , FE D:1012 , FE D:1013 , FE D:1014 , HOH D:1033 , HOH D:1171
BINDING SITE FOR RESIDUE OXY D 1015
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1oqua_ (A:)
1b: SCOP_d1oqub_ (B:)
1c: SCOP_d1oquc_ (C:)
1d: SCOP_d1oqud_ (D:)
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(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Ferritin-like
(489)
Family
:
Ribonucleotide reductase-like
(185)
Protein domain
:
Ribonucleotide reductase R2
(45)
Corynebacterium ammoniagenes [TaxId: 1697]
(6)
1a
d1oqua_
A:
1b
d1oqub_
B:
1c
d1oquc_
C:
1d
d1oqud_
D:
[
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1oquC00 (C:2-329)
1b: CATH_1oquB00 (B:2-297)
1c: CATH_1oquD00 (D:2-297)
1d: CATH_1oquA00 (A:2-297)
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)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Ribonucleotide Reductase, subunit A
(86)
Homologous Superfamily
:
Ribonucleotide Reductase, subunit A
(86)
Corynebacterium ammoniagenes. Organism_taxid: 1697.
(4)
1a
1oquC00
C:2-329
1b
1oquB00
B:2-297
1c
1oquD00
D:2-297
1d
1oquA00
A:2-297
[
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Ribonuc_red_sm_1oquD01 (D:13-291)
1b: PFAM_Ribonuc_red_sm_1oquD02 (D:13-291)
1c: PFAM_Ribonuc_red_sm_1oquD03 (D:13-291)
1d: PFAM_Ribonuc_red_sm_1oquD04 (D:13-291)
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(
)
Clan
:
Ferritin
(185)
Family
:
Ribonuc_red_sm
(41)
Corynebacterium ammoniagenes (Brevibacterium ammoniagenes)
(5)
1a
Ribonuc_red_sm-1oquD01
D:13-291
1b
Ribonuc_red_sm-1oquD02
D:13-291
1c
Ribonuc_red_sm-1oquD03
D:13-291
1d
Ribonuc_red_sm-1oquD04
D:13-291
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Asym.Unit (222 KB)
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