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1ZLQ
Biol. Unit 1
Info
Asym.Unit (367 KB)
Biol.Unit 1 (185 KB)
Biol.Unit 2 (181 KB)
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(1)
Title
:
CRYSTALLOGRAPHIC AND SPECTROSCOPIC EVIDENCE FOR HIGH AFFINITY BINDING OF FE EDTA (H2O)- TO THE PERIPLASMIC NICKEL TRANSPORTER NIKA
Authors
:
M. V. Cherrier, L. Martin, C. Cavazza, L. Jacquamet, D. Lemaire, J. Gail J. C. Fontecilla Camps
Date
:
09 May 05 (Deposition) - 02 Aug 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Nickel, Edta, Transport, Bacteria, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. V. Cherrier, L. Martin, C. Cavazza, L. Jacquamet, D. Lemaire, J. Gaillard, J. C. Fontecilla Camps
Crystallographic And Spectroscopic Evidence For High Affinity Binding Of Feedta(H(2)O)(-) To The Periplasmic Nickel Transporter Nika
J. Am. Chem. Soc. V. 127 10075 2005
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Hetero Components
(5, 12)
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)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
3a: 2,3-DIHYDROXY-1,4-DITHIOBUTANE (DTTa)
4a: {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL... (EDTa)
4b: {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL... (EDTb)
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)
7a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
6
Ligand/Ion
ACETATE ION
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
DTT
1
Ligand/Ion
2,3-DIHYDROXY-1,4-DITHIOBUTANE
4
EDT
1
Ligand/Ion
{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID
5
FE
-1
Ligand/Ion
FE (III) ION
6
GOL
3
Ligand/Ion
GLYCEROL
7
SO4
1
Ligand/Ion
SULFATE ION
[
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Sites
(17, 17)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC7 (SOFTWARE)
05: AC8 (SOFTWARE)
06: AC9 (SOFTWARE)
07: BC1 (SOFTWARE)
08: BC3 (SOFTWARE)
09: BC4 (SOFTWARE)
10: BC5 (SOFTWARE)
11: BC6 (SOFTWARE)
12: BC8 (SOFTWARE)
13: BC9 (SOFTWARE)
14: CC2 (SOFTWARE)
15: CC3 (SOFTWARE)
16: CC5 (SOFTWARE)
17: CC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
EDT A:1513
BINDING SITE FOR RESIDUE FE A 1501
02
AC3
SOFTWARE
PRO A:11 , GLY A:219 , ASN A:220 , GLY A:222 , LEU A:223 , HOH A:1927
BINDING SITE FOR RESIDUE ACT A 1502
03
AC5
SOFTWARE
LYS A:52 , ARG A:68 , ASP A:69 , ASP A:70 , HOH A:1883
BINDING SITE FOR RESIDUE ACT A 1503
04
AC7
SOFTWARE
ASN A:261 , GLU A:262 , LEU A:263 , HOH A:1576 , HOH A:1589 , HOH A:1877
BINDING SITE FOR RESIDUE ACT A 1504
05
AC8
SOFTWARE
ASN A:235 , ALA A:237 , PHE A:419 , GLN A:423 , HOH A:1600 , HOH A:1709
BINDING SITE FOR RESIDUE ACT A 1505
06
AC9
SOFTWARE
ASN A:482 , GLN A:496 , HOH A:1801 , ASP B:43
BINDING SITE FOR RESIDUE ACT A 1506
07
BC1
SOFTWARE
GLN A:385 , PHE A:394 , HIS A:395 , ARG A:396 , HOH A:1648
BINDING SITE FOR RESIDUE ACT A 1507
08
BC3
SOFTWARE
ARG A:384 , HOH A:1805 , HOH A:1897 , HOH A:1908 , LEU B:430 , ARG B:457
BINDING SITE FOR RESIDUE SO4 A 1508
09
BC4
SOFTWARE
GLN A:26
BINDING SITE FOR RESIDUE CL A 1509
10
BC5
SOFTWARE
ASP A:331 , ARG A:365
BINDING SITE FOR RESIDUE CL A 1510
11
BC6
SOFTWARE
ARG A:97 , HOH A:1642 , LYS B:306 , LYS B:314
BINDING SITE FOR RESIDUE CL A 1511
12
BC8
SOFTWARE
PHE A:229 , SER A:233 , ASN B:302
BINDING SITE FOR RESIDUE CL A 1512
13
BC9
SOFTWARE
TYR A:22 , MET A:27 , ARG A:97 , TRP A:100 , ARG A:137 , TRP A:398 , HIS A:416 , THR A:490 , FE A:1501 , HOH A:1647 , HOH A:1747 , HOH A:1903 , HOH A:1937
BINDING SITE FOR RESIDUE EDT A 1513
14
CC2
SOFTWARE
ARG A:89 , LEU A:92 , ARG A:95 , VAL A:108 , ASP A:109 , VAL A:110 , ASN A:281 , GLU A:358 , ILE A:359 , ALA A:362 , HOH A:1972 , HOH A:1976 , HOH A:1987
BINDING SITE FOR RESIDUE DTT A 1514
15
CC3
SOFTWARE
LEU A:167 , GLN A:168 , HOH A:1683 , THR B:211 , ASP B:213
BINDING SITE FOR RESIDUE GOL A 1515
16
CC5
SOFTWARE
LYS A:148 , ASN A:149 , LYS A:157 , HOH A:1887 , HOH A:1931
BINDING SITE FOR RESIDUE GOL A 1516
17
CC6
SOFTWARE
LYS A:111 , GLU A:358 , GLN A:361 , SER A:372 , LEU A:373
BINDING SITE FOR RESIDUE GOL A 1517
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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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_d1zlqa1 (A:3-501)
1b: SCOP_d1zlqb_ (B:)
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Protein Domains
(
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(
)
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
d1zlqa1
A:3-501
1b
d1zlqb_
B:
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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
(1, 2)
Info
all PFAM domains
1a: PFAM_SBP_bac_5_1zlqB01 (B:45-419)
1b: PFAM_SBP_bac_5_1zlqB02 (B:45-419)
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)
(
)
Clan
:
PBP
(391)
Family
:
SBP_bac_5
(33)
Escherichia coli (strain K12)
(12)
1a
SBP_bac_5-1zlqB01
B:45-419
1b
SBP_bac_5-1zlqB02
B:45-419
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Chain A
Asymmetric Unit 1
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Show PDB file:
Asym.Unit (367 KB)
Header - Asym.Unit
Biol.Unit 1 (185 KB)
Header - Biol.Unit 1
Biol.Unit 2 (181 KB)
Header - Biol.Unit 2
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