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3DP8
Asym. Unit
Info
Asym.Unit (261 KB)
Biol.Unit 1 (89 KB)
Biol.Unit 2 (89 KB)
Biol.Unit 3 (87 KB)
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(1)
Title
:
STRUCTURAL CHARACTERIZATION OF A PUTATIVE ENDOGENOUS METAL CHELATOR IN THE PERIPLASMIC NICKEL TRANSPORTER NIKA (NICKEL BUTANE-1,2,4-TRICARBOXYLATE FORM)
Authors
:
M. V. Cherrier, C. Cavazza, C. Bochot, D. Lemaire, J. C. Fontecilla-Cam
Date
:
07 Jul 08 (Deposition) - 16 Sep 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Nickel, Nickellophore, Butane-1, 2, 4-Tricarboxylate, Transport, Metal Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. V. Cherrier, C. Cavazza, C. Bochot, D. Lemaire, J. C. Fontecilla-Camps
Structural Characterization Of A Putative Endogenous Metal Chelator In The Periplasmic Nickel Transporter Nika
Biochemistry V. 47 9937 2008
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Hetero Components
(6, 33)
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: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
2g: CHLORIDE ION (CLg)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
3h: GLYCEROL (GOLh)
4a: (2R)-BUTANE-1,2,4-TRICARBOXYLIC AC... (HCTa)
4b: (2R)-BUTANE-1,2,4-TRICARBOXYLIC AC... (HCTb)
4c: (2R)-BUTANE-1,2,4-TRICARBOXYLIC AC... (HCTc)
5a: NICKEL (II) ION (NIa)
5b: NICKEL (II) ION (NIb)
5c: NICKEL (II) ION (NIc)
6a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
11
Ligand/Ion
ACETATE ION
2
CL
7
Ligand/Ion
CHLORIDE ION
3
GOL
8
Ligand/Ion
GLYCEROL
4
HCT
3
Ligand/Ion
(2R)-BUTANE-1,2,4-TRICARBOXYLIC ACID
5
NI
3
Ligand/Ion
NICKEL (II) ION
6
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: CC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS B:416
BINDING SITE FOR RESIDUE NI B 503
02
AC2
SOFTWARE
HIS C:416
BINDING SITE FOR RESIDUE NI C 503
03
AC3
SOFTWARE
THR C:292 , LEU C:293 , LEU C:455 , HIS C:459 , TYR C:464
BINDING SITE FOR RESIDUE ACT C 504
04
AC4
SOFTWARE
LYS C:330 , ASP C:331 , ILE C:332 , ARG C:365
BINDING SITE FOR RESIDUE ACT C 505
05
AC5
SOFTWARE
SER A:57 , GLU A:58
BINDING SITE FOR RESIDUE ACT A 505
06
AC6
SOFTWARE
GLU B:221 , LEU B:226 , PHE B:229 , LEU B:283 , THR B:286 , MET B:473
BINDING SITE FOR RESIDUE ACT B 504
07
AC7
SOFTWARE
GLN C:385 , HIS C:395 , ARG C:396 , TRP C:398 , HIS C:416
BINDING SITE FOR RESIDUE ACT C 506
08
AC8
SOFTWARE
GLN A:288 , THR B:286 , GLN B:288
BINDING SITE FOR RESIDUE ACT A 506
09
AC9
SOFTWARE
ARG B:341 , LYS C:433
BINDING SITE FOR RESIDUE ACT B 505
10
BC1
SOFTWARE
TYR B:271 , LYS B:306 , PRO B:307 , HIS B:459
BINDING SITE FOR RESIDUE ACT B 506
11
BC2
SOFTWARE
THR B:8 , ALA B:9 , LEU B:216 , LEU B:217 , TYR B:218 , LEU B:223
BINDING SITE FOR RESIDUE ACT B 507
12
BC3
SOFTWARE
ASP A:93 , ASN A:94 , ARG A:95 , GLN A:96 , GLN C:446
BINDING SITE FOR RESIDUE ACT A 507
13
BC4
SOFTWARE
GLN A:361 , SER A:372 , LEU A:373
BINDING SITE FOR RESIDUE SO4 A 508
14
BC5
SOFTWARE
THR B:441 , HIS B:442
BINDING SITE FOR RESIDUE CL B 508
15
BC6
SOFTWARE
LEU B:293 , HIS B:459
BINDING SITE FOR RESIDUE CL B 509
16
BC7
SOFTWARE
TYR B:22 , ARG B:97 , ARG B:137 , TRP B:398 , HIS B:416
BINDING SITE FOR RESIDUE HCT B 511
17
BC8
SOFTWARE
TYR A:22 , ARG A:97 , TRP A:100 , ARG A:137 , TRP A:398 , HIS A:416
BINDING SITE FOR RESIDUE HCT A 511
18
BC9
SOFTWARE
TYR C:22 , MET C:27 , ARG C:97 , TRP C:100 , ARG C:137 , ARG C:396 , TRP C:398 , HIS C:416
BINDING SITE FOR RESIDUE HCT C 509
19
CC1
SOFTWARE
ASN A:274 , LYS A:276 , ASP A:280 , LYS A:316 , GLU A:320 , LEU A:326 , ARG A:333
BINDING SITE FOR RESIDUE GOL A 512
20
CC2
SOFTWARE
PRO B:48 , LYS B:52 , SER B:53 , TRP B:54
BINDING SITE FOR RESIDUE GOL B 512
21
CC3
SOFTWARE
THR A:349 , GLU A:376 , GLU A:377 , GLU A:378
BINDING SITE FOR RESIDUE GOL A 513
22
CC4
SOFTWARE
ASN B:254 , ALA B:256 , LYS B:257 , ASP B:387 , GLY B:388 , GLN B:420 , GLN B:423
BINDING SITE FOR RESIDUE GOL B 513
23
CC5
SOFTWARE
SER B:57 , GLU B:58
BINDING SITE FOR RESIDUE GOL B 514
24
CC6
SOFTWARE
ALA A:42 , ASP A:43 , GLN B:41 , ALA B:42 , TYR B:485 , PRO B:487
BINDING SITE FOR RESIDUE GOL A 514
25
CC7
SOFTWARE
LYS B:354 , GLU B:358
BINDING SITE FOR RESIDUE GOL A 515
26
CC8
SOFTWARE
ARG A:389 , GLU B:358 , GLN B:361 , SER B:372 , LEU B:373
BINDING SITE FOR RESIDUE GOL B 515
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 3)
Info
All PROSITE Patterns/Profiles
1: SBP_BACTERIAL_5 (A:51-73,B:51-73,C: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
3
A:51-73
B:51-73
C: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.
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d3dp8a_ (A:)
1b: SCOP_d3dp8b_ (B:)
1c: SCOP_d3dp8c_ (C:)
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Classes
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)
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
d3dp8a_
A:
1b
d3dp8b_
B:
1c
d3dp8c_
C:
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
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Asymmetric Unit 1
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (261 KB)
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