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Zinc in PDB 3qvy: Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks

Protein crystallography data

The structure of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks, PDB code: 3qvy was solved by E.N.Salgado, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.51 / 2.30
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 52.088, 52.088, 253.943, 90.00, 90.00, 120.00
R / Rfree (%) 24.2 / 28.6

Other elements in 3qvy:

The structure of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks (pdb code 3qvy). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 13 binding sites of Zinc where determined in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks, PDB code: 3qvy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 13 in 3qvy

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Zinc binding site 1 out of 13 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:23.4
occ:1.00
NE2 D:HIS63 1.8 26.8 1.0
NE2 A:HIS73 1.9 24.8 1.0
OD2 C:ASP74 2.0 28.5 1.0
NE2 A:HIS77 2.0 25.8 1.0
CE1 D:HIS63 2.6 25.9 1.0
CE1 A:HIS73 2.8 25.2 1.0
CG C:ASP74 2.8 26.8 1.0
CE1 A:HIS77 2.9 24.8 1.0
CD2 D:HIS63 3.0 26.2 1.0
CD2 A:HIS73 3.1 23.8 1.0
OD1 C:ASP74 3.1 29.8 1.0
CD2 A:HIS77 3.1 23.9 1.0
ND1 D:HIS63 3.8 28.4 1.0
ND1 A:HIS73 4.0 26.0 1.0
CG D:HIS63 4.0 28.0 1.0
ND1 A:HIS77 4.1 23.9 1.0
CG A:HIS73 4.1 24.8 1.0
CD1 D:ILE67 4.2 26.9 1.0
CG A:HIS77 4.2 25.2 1.0
CB C:ASP74 4.3 25.5 1.0
CA C:ASP74 4.8 25.6 1.0
O C:ASP74 5.0 25.7 1.0

Zinc binding site 2 out of 13 in 3qvy

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Zinc binding site 2 out of 13 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn107

b:38.9
occ:1.00
OD2 A:ASP39 2.1 41.7 1.0
O A:ALA1 2.1 38.9 1.0
N A:ALA1 2.1 39.8 1.0
CG A:ASP39 2.7 37.6 1.0
OD1 A:ASP39 2.7 40.2 1.0
C A:ALA1 2.8 38.8 1.0
CA A:ALA1 2.9 39.1 1.0
CB A:ALA1 3.6 39.7 1.0
N A:ASP2 4.1 38.2 1.0
CB A:ASP39 4.1 35.4 1.0
O A:HOH118 4.1 25.8 1.0
ND2 A:ASN6 4.5 33.2 1.0
CA A:ASP2 4.8 38.2 1.0
OD1 A:ASN6 4.9 33.2 1.0

Zinc binding site 3 out of 13 in 3qvy

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Zinc binding site 3 out of 13 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn108

b:54.6
occ:1.00
O2A A:HEM150 2.0 42.0 1.0
OE1 A:GLU4 2.3 46.6 1.0
CD A:GLU4 2.5 46.1 1.0
OE2 A:GLU4 2.9 49.2 1.0
CGA A:HEM150 3.1 36.6 1.0
ZN A:ZN110 3.2 57.9 1.0
CG A:GLU4 3.5 42.5 1.0
O1A A:HEM150 3.5 38.1 1.0
O2D A:HEM150 3.9 30.2 1.0
CBA A:HEM150 4.3 33.8 1.0
CGD A:HEM150 4.8 30.8 1.0
CB A:GLU4 5.0 39.1 1.0

Zinc binding site 4 out of 13 in 3qvy

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Zinc binding site 4 out of 13 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn109

b:81.0
occ:1.00
OD1 A:ASP2 2.1 42.8 1.0
OD1 A:ASP5 2.3 44.1 1.0
CG A:ASP2 3.1 41.6 1.0
CG A:ASP5 3.3 42.5 1.0
OD2 A:ASP2 3.4 42.5 1.0
OD2 A:ASP5 3.7 47.0 1.0
CB A:ASP2 4.4 38.6 1.0
CB A:ASP5 4.6 38.9 1.0
N A:ASP5 4.9 37.9 1.0
CB A:GLU4 5.0 39.1 1.0

Zinc binding site 5 out of 13 in 3qvy

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Zinc binding site 5 out of 13 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn110

b:57.9
occ:1.00
OE2 A:GLU4 2.1 49.2 1.0
CD A:GLU4 3.0 46.1 1.0
OE1 A:GLU4 3.1 46.6 1.0
ZN A:ZN108 3.2 54.6 1.0
O2A A:HEM150 4.5 42.0 1.0
O1A A:HEM150 4.5 38.1 1.0
CG A:GLU4 4.5 42.5 1.0
CGA A:HEM150 5.0 36.6 1.0

Zinc binding site 6 out of 13 in 3qvy

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Zinc binding site 6 out of 13 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn500

b:25.3
occ:1.00
NE2 B:HIS73 1.8 25.2 1.0
NE2 B:HIS77 2.1 25.5 1.0
NE2 C:HIS63 2.2 26.4 1.0
OD2 D:ASP74 2.2 28.6 1.0
CE1 B:HIS73 2.5 25.3 1.0
OD1 D:ASP74 2.5 30.0 1.0
CG D:ASP74 2.7 26.3 1.0
CD2 C:HIS63 3.0 25.9 1.0
CD2 B:HIS77 3.0 24.2 1.0
CD2 B:HIS73 3.0 23.9 1.0
CE1 B:HIS77 3.1 24.9 1.0
CE1 C:HIS63 3.3 26.2 1.0
ND1 B:HIS73 3.7 26.3 1.0
CG B:HIS73 4.0 25.1 1.0
CB D:ASP74 4.2 25.8 1.0
CG B:HIS77 4.2 25.4 1.0
ND1 B:HIS77 4.2 23.9 1.0
CG C:HIS63 4.2 27.8 1.0
ND1 C:HIS63 4.3 28.4 1.0
CD1 C:ILE67 4.7 27.2 1.0
CA D:ASP74 4.9 25.6 1.0
O D:ASP74 5.0 25.5 1.0

Zinc binding site 7 out of 13 in 3qvy

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Zinc binding site 7 out of 13 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn107

b:42.4
occ:1.00
OE2 B:GLU4 2.0 48.8 1.0
O2A B:HEM150 2.0 46.2 1.0
CD B:GLU4 2.4 45.8 1.0
OE1 B:GLU4 2.4 46.5 1.0
ZN B:ZN108 3.0 53.8 1.0
CGA B:HEM150 3.2 46.8 1.0
CG B:GLU4 3.6 42.4 1.0
CBA B:HEM150 3.9 46.1 1.0
O1A B:HEM150 4.2 44.6 1.0
CAA B:HEM150 4.4 40.5 1.0
O2D B:HEM150 4.6 41.5 1.0
OE2 B:GLU8 4.6 47.8 1.0
CB B:GLU4 4.8 39.4 1.0

Zinc binding site 8 out of 13 in 3qvy

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Zinc binding site 8 out of 13 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn108

b:53.8
occ:1.00
ZN B:ZN107 3.0 42.4 1.0
O2A B:HEM150 3.7 46.2 1.0
CBA B:HEM150 4.2 46.1 1.0
CGA B:HEM150 4.3 46.8 1.0
OE1 B:GLU4 4.7 46.5 1.0

Zinc binding site 9 out of 13 in 3qvy

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Zinc binding site 9 out of 13 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn500

b:25.2
occ:1.00
NE2 B:HIS63 1.8 26.7 1.0
NE2 C:HIS77 1.9 25.9 1.0
OD2 A:ASP74 1.9 28.6 1.0
NE2 C:HIS73 2.0 25.0 1.0
CE1 B:HIS63 2.6 25.9 1.0
CE1 C:HIS77 2.8 24.8 1.0
CG A:ASP74 2.8 26.9 1.0
CE1 C:HIS73 2.9 25.1 1.0
CD2 B:HIS63 3.0 26.3 1.0
CD2 C:HIS77 3.0 24.0 1.0
OD1 A:ASP74 3.1 30.0 1.0
CD2 C:HIS73 3.1 24.2 1.0
ND1 B:HIS63 3.8 28.1 1.0
ND1 C:HIS77 4.0 23.7 1.0
CG B:HIS63 4.0 28.1 1.0
ND1 C:HIS73 4.0 25.8 1.0
CG C:HIS77 4.1 25.1 1.0
CG C:HIS73 4.1 24.7 1.0
CD1 B:ILE67 4.2 26.9 1.0
CB A:ASP74 4.3 25.4 1.0
CA A:ASP74 4.8 25.7 1.0

Zinc binding site 10 out of 13 in 3qvy

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Zinc binding site 10 out of 13 in the Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Zn-RIDC1 Complex Stabilized By Bmoe Crosslinks within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn107

b:40.2
occ:1.00
N C:ALA1 1.9 39.9 1.0
O C:ALA1 2.1 39.1 1.0
OD2 C:ASP39 2.1 41.9 1.0
C C:ALA1 2.7 38.9 1.0
CA C:ALA1 2.7 39.1 1.0
CG C:ASP39 2.8 37.7 1.0
OD1 C:ASP39 2.9 40.2 1.0
CB C:ALA1 3.6 39.8 1.0
N C:ASP2 4.0 38.2 1.0
CB C:ASP39 4.3 35.2 1.0
ND2 C:ASN6 4.7 33.1 1.0
CA C:ASP2 4.8 38.1 1.0
OD1 C:ASN6 5.0 33.3 1.0

Reference:

E.N.Salgado, J.D.Brodin, M.M.To, F.A.Tezcan. Templated Construction of A Zn-Selective Protein Dimerization Motif. Inorg.Chem. V. 50 6323 2011.
ISSN: ISSN 0020-1669
PubMed: 21648390
DOI: 10.1021/IC200746M
Page generated: Wed Dec 16 04:46:07 2020

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