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3NMJ
Asym. Unit
Info
Asym.Unit (77 KB)
Biol.Unit 1 (20 KB)
Biol.Unit 2 (20 KB)
Biol.Unit 3 (19 KB)
Biol.Unit 4 (20 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF A NICKEL MEDIATED DIMER FOR THE PHENANTHROLINE-MODIFIED CYTOCHROME CB562 VARIANT, MBP-PHEN2
Authors
:
R. J. Radford, F. A. Tezcan
Date
:
22 Jun 10 (Deposition) - 24 Nov 10 (Release) - 29 Dec 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
4-Helix-Bundle, Electron Transport
(Keyword Search:
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Reference
:
R. J. Radford, M. Lawrenz, P. C. Nguyen, J. A. Mccammon, F. A. Tezcan
Porous Protein Frameworks With Unsaturated Metal Centers In Sterically Encumbered Coordination Sites.
Chem. Commun. (Camb. ) V. 47 313 2011
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Hetero Components
(3, 10)
Info
All Hetero Components
1a: PROTOPORPHYRIN IX CONTAINING FE (HEMa)
1b: PROTOPORPHYRIN IX CONTAINING FE (HEMb)
1c: PROTOPORPHYRIN IX CONTAINING FE (HEMc)
1d: PROTOPORPHYRIN IX CONTAINING FE (HEMd)
2a: NICKEL (II) ION (NIa)
2b: NICKEL (II) ION (NIb)
3a: N-1,10-PHENANTHROLIN-5-YLACETAMIDE (PXXa)
3b: N-1,10-PHENANTHROLIN-5-YLACETAMIDE (PXXb)
3c: N-1,10-PHENANTHROLIN-5-YLACETAMIDE (PXXc)
3d: N-1,10-PHENANTHROLIN-5-YLACETAMIDE (PXXd)
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Label:
No.
Name
Count
Type
Full Name
1
HEM
4
Ligand/Ion
PROTOPORPHYRIN IX CONTAINING FE
2
NI
2
Ligand/Ion
NICKEL (II) ION
3
PXX
4
Ligand/Ion
N-1,10-PHENANTHROLIN-5-YLACETAMIDE
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Sites
(10, 10)
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)
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No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:4 , MET A:7 , ASN A:11 , PRO A:46 , PHE A:61 , PHE A:65 , CYS A:98 , CYS A:101 , HIS A:102 , TYR A:105 , ARG A:106
BINDING SITE FOR RESIDUE HEM A 150
02
AC2
SOFTWARE
ASP A:54 , CYS A:59 , LYS B:42 , THR C:44 , PRO C:53 , MET C:58 , PXX C:151 , NI C:152
BINDING SITE FOR RESIDUE PXX A 151
03
AC3
SOFTWARE
HOH A:107 , PXX A:151 , PXX C:151
BINDING SITE FOR RESIDUE NI C 152
04
AC4
SOFTWARE
GLU B:4 , MET B:7 , PRO B:46 , PHE B:61 , PHE B:65 , CYS B:98 , CYS B:101 , HIS B:102 , ARG B:106
BINDING SITE FOR RESIDUE HEM B 150
05
AC5
SOFTWARE
GLN A:41 , GLN B:41 , LYS B:42 , ALA B:43 , PRO B:53 , MET B:58 , CYS B:59 , ALA B:62 , NI B:152 , PXX D:151
BINDING SITE FOR RESIDUE PXX B 151
06
AC6
SOFTWARE
PXX B:151 , HOH D:107 , PXX D:151
BINDING SITE FOR RESIDUE NI B 152
07
AC7
SOFTWARE
LEU C:3 , MET C:7 , PRO C:45 , PHE C:61 , PHE C:65 , CYS C:98 , CYS C:101 , HIS C:102
BINDING SITE FOR RESIDUE HEM C 150
08
AC8
SOFTWARE
PXX A:151 , GLN C:41 , LYS C:42 , ALA C:43 , PRO C:53 , MET C:58 , CYS C:59 , ALA C:62 , NI C:152 , GLN D:41
BINDING SITE FOR RESIDUE PXX C 151
09
AC9
SOFTWARE
GLU D:4 , MET D:7 , PRO D:46 , PHE D:61 , PHE D:65 , THR D:97 , CYS D:98 , CYS D:101 , HIS D:102 , TYR D:105 , ARG D:106
BINDING SITE FOR RESIDUE HEM D 150
10
BC1
SOFTWARE
THR B:44 , PRO B:53 , MET B:58 , PXX B:151 , NI B:152 , LYS C:42 , PRO D:53 , ASP D:54 , CYS D:59
BINDING SITE FOR RESIDUE PXX D 151
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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Exons
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All Exons
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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_d3nmja_ (A:)
1b: SCOP_d3nmjb_ (B:)
1c: SCOP_d3nmjc_ (C:)
1d: SCOP_d3nmjd_ (D:)
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Class
:
All alpha proteins
(14657)
Fold
:
Four-helical up-and-down bundle
(308)
Superfamily
:
Cytochromes
(82)
Family
:
Cytochrome b562
(38)
Protein domain
:
automated matches
(32)
Escherichia coli [TaxId: 562]
(31)
1a
d3nmja_
A:
1b
d3nmjb_
B:
1c
d3nmjc_
C:
1d
d3nmjd_
D:
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Cytochrom_B562_3nmjD01 (D:1-106)
1b: PFAM_Cytochrom_B562_3nmjD02 (D:1-106)
1c: PFAM_Cytochrom_B562_3nmjD03 (D:1-106)
1d: PFAM_Cytochrom_B562_3nmjD04 (D:1-106)
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Clan
:
no clan defined [family: Cytochrom_B562]
(14)
Family
:
Cytochrom_B562
(14)
Escherichia coli
(13)
1a
Cytochrom_B562-3nmjD01
D:1-106
1b
Cytochrom_B562-3nmjD02
D:1-106
1c
Cytochrom_B562-3nmjD03
D:1-106
1d
Cytochrom_B562-3nmjD04
D:1-106
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Asymmetric Unit 1
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Asym.Unit (77 KB)
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Biol.Unit 1 (20 KB)
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Biol.Unit 2 (20 KB)
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Biol.Unit 3 (19 KB)
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