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3MZB
Biol. Unit 1
Info
Asym.Unit (186 KB)
Biol.Unit 1 (94 KB)
Biol.Unit 2 (90 KB)
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(1)
Title
:
X-RAY STRUCTURE OF NIKA IN COMPLEX WITH THE DOUBLY HYDROXYLATED IRON COMPLEX, 1-O2
Authors
:
C. Cavazza, C. Bochot, P. Rousselot-Pailley, P. Carpentier, M. V. Cher L. Martin, C. Marchi-Delapierre, J. C. Fontecilla-Camps, S. Menage
Date
:
12 May 10 (Deposition) - 09 Feb 11 (Release) - 09 Feb 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Protein-Bound Iron Complex, Transport Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Cavazza, C. Bochot, P. Rousselot-Pailley, P. Carpentier, M. V. Cherrier, L. Martin, C. Marchi-Delapierre, J. C. Fontecilla-Camps, S. Menage
Crystallographic Snapshots Of The Reaction Of Aromatic C-H With O(2) Catalysed By A Protein-Bound Iron Complex
Nat. Chem. V. 2 1069 2010
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Hetero Components
(5, 20)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
1g: ACETATE ION (ACTg)
1h: ACETATE ION (ACTh)
1i: ACETATE ION (ACTi)
1j: ACETATE ION (ACTj)
1k: ACETATE ION (ACTk)
2a: 2-[2-[CARBOXYMETHYL-[(2-HYDROXYPHE... (BHRa)
2b: 2-[2-[CARBOXYMETHYL-[(2-HYDROXYPHE... (BHRb)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
3d: CHLORIDE ION (CLd)
3e: CHLORIDE ION (CLe)
4a: DITHIANE DIOL (DTDa)
4b: DITHIANE DIOL (DTDb)
5a: FE (III) ION (FEa)
5b: FE (III) ION (FEb)
6a: GLYCEROL (GOLa)
6b: GLYCEROL (GOLb)
6c: GLYCEROL (GOLc)
6d: GLYCEROL (GOLd)
6e: GLYCEROL (GOLe)
6f: GLYCEROL (GOLf)
6g: GLYCEROL (GOLg)
6h: GLYCEROL (GOLh)
6i: GLYCEROL (GOLi)
6j: GLYCEROL (GOLj)
6k: GLYCEROL (GOLk)
6l: GLYCEROL (GOLl)
6m: GLYCEROL (GOLm)
7a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
7
Ligand/Ion
ACETATE ION
2
BHR
1
Ligand/Ion
2-[2-[CARBOXYMETHYL-[(2-HYDROXYPHENYL)METHYL]AMINO]ETHYL-[(2,3-DIHYDROXYPHENYL)METHYL]AMINO]ETHANOIC ACID
3
CL
-1
Ligand/Ion
CHLORIDE ION
4
DTD
1
Ligand/Ion
DITHIANE DIOL
5
FE
-1
Ligand/Ion
FE (III) ION
6
GOL
10
Ligand/Ion
GLYCEROL
7
SO4
1
Ligand/Ion
SULFATE ION
[
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Sites
(26, 26)
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: CC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:270 , ASP A:291 , HIS A:459 , ALA A:462 , TYR A:464 , HOH A:568 , HOH A:600
BINDING SITE FOR RESIDUE ACT A 502
02
AC2
SOFTWARE
LYS A:52 , ARG A:68 , ASP A:69 , ASP A:70
BINDING SITE FOR RESIDUE ACT A 503
03
AC3
SOFTWARE
ASN A:302 , GLY A:304 , PHE B:229 , ALA B:230 , SER B:233 , THR B:286
BINDING SITE FOR RESIDUE ACT A 504
04
AC4
SOFTWARE
ASN A:261 , GLU A:262 , LEU A:263 , GOL A:516
BINDING SITE FOR RESIDUE ACT A 505
05
AC5
SOFTWARE
ASN A:235 , ALA A:237 , PHE A:419 , GLN A:423 , HOH A:676
BINDING SITE FOR RESIDUE ACT A 506
06
AC6
SOFTWARE
ASN A:482 , GLN A:496
BINDING SITE FOR RESIDUE ACT A 507
07
AC7
SOFTWARE
GLN A:385 , PHE A:394 , HIS A:395 , ARG A:396 , HOH A:759
BINDING SITE FOR RESIDUE ACT A 508
08
AC8
SOFTWARE
ARG A:384 , ARG A:389 , HOH A:811 , LEU B:430 , ARG B:457
BINDING SITE FOR RESIDUE SO4 A 509
09
AC9
SOFTWARE
ALA A:158 , LEU A:167 , GLN A:168 , HOH A:599 , THR B:211 , ASP B:213
BINDING SITE FOR RESIDUE GOL A 510
10
BC1
SOFTWARE
LYS A:148 , ASN A:149 , LYS A:157 , HOH A:932
BINDING SITE FOR RESIDUE GOL A 511
11
BC2
SOFTWARE
SER A:243 , ILE A:246 , MET A:472 , TYR A:485 , ALA A:486 , HOH A:654 , HOH A:743
BINDING SITE FOR RESIDUE GOL A 512
12
BC3
SOFTWARE
LEU A:92 , VAL A:108 , ASP A:109 , VAL A:110 , ASN A:281
BINDING SITE FOR RESIDUE GOL A 513
13
BC4
SOFTWARE
ARG A:68 , ASP A:69 , PRO A:78 , PHE A:79 , ASP A:80 , LYS A:115 , THR A:116 , HOH A:606 , HOH A:797 , HOH A:860
BINDING SITE FOR RESIDUE GOL A 514
14
BC5
SOFTWARE
GLU A:86 , ARG A:89 , PRO A:144 , PHE A:147 , HIS A:150 , HOH A:830
BINDING SITE FOR RESIDUE GOL A 515
15
BC6
SOFTWARE
THR A:255 , ASN A:261 , ARG A:266 , GLY A:424 , LEU A:425 , ALA A:426 , ACT A:505 , HOH A:660
BINDING SITE FOR RESIDUE GOL A 516
16
BC7
SOFTWARE
THR A:23 , GLN A:26
BINDING SITE FOR RESIDUE CL A 517
17
BC8
SOFTWARE
ASP A:331 , ARG A:365
BINDING SITE FOR RESIDUE CL A 518
18
BC9
SOFTWARE
ARG A:97 , LYS B:314
BINDING SITE FOR RESIDUE CL A 519
19
CC1
SOFTWARE
TYR A:22 , THR A:23 , MET A:27 , ARG A:97 , TRP A:100 , ARG A:137 , TRP A:398 , THR A:490 , FE A:521 , HOH A:582 , HOH A:618
BINDING SITE FOR RESIDUE BHR A 520
20
CC2
SOFTWARE
BHR A:520
BINDING SITE FOR RESIDUE FE A 521
21
CC3
SOFTWARE
TRP A:10 , PRO A:11 , ARG A:205 , GLY A:219 , ASN A:220 , GLY A:222
BINDING SITE FOR RESIDUE DTD A 522
22
CC4
SOFTWARE
TRP A:54
BINDING SITE FOR RESIDUE CL A 523
23
CC5
SOFTWARE
THR A:211 , LYS A:433 , HOH A:571
BINDING SITE FOR RESIDUE GOL A 525
24
CC6
SOFTWARE
ASP A:453 , THR A:456 , ARG A:457 , ASP A:460 , HOH A:825
BINDING SITE FOR RESIDUE GOL A 526
25
CC7
SOFTWARE
PHE A:229 , ALA A:230 , LEU A:242 , THR A:286 , ASN B:302
BINDING SITE FOR RESIDUE GOL A 527
26
CC9
SOFTWARE
ASN A:75 , GLY A:76 , THR B:203 , PRO B:225 , ASP B:227 , THR B:228
BINDING SITE FOR RESIDUE ACT B 503
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: SBP_BACTERIAL_5 (A:51-73)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SBP_BACTERIAL_5
PS01040
Bacterial extracellular solute-binding proteins, family 5 signature.
NIKA_ECOLI
73-95
1
A:51-73
-
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3mzba_ (A:)
1b: SCOP_d3mzbb_ (B:)
View:
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Label:
Classes
(
)
(
)
Folds
(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Periplasmic binding protein-like II
(813)
Superfamily
:
Periplasmic binding protein-like II
(813)
Family
:
Phosphate binding protein-like
(463)
Protein domain
:
Nickel-binding periplasmic protein NikA
(18)
Escherichia coli [TaxId: 562]
(18)
1a
d3mzba_
A:
1b
d3mzbb_
B:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Atom Selection
(currently selected atoms:
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Protein
Nucleic
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Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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Example Command
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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)
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