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Zinc in PDB 2ox8: Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain.

Protein crystallography data

The structure of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain., PDB code: 2ox8 was solved by W.I.Weis, H.Feinberg, K.Drickamer, M.E.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.92 / 2.50
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 80.422, 80.422, 67.159, 90.00, 90.00, 120.00
R / Rfree (%) 23.3 / 30.8

Other elements in 2ox8:

The structure of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. also contains other interesting chemical elements:

Chlorine (Cl) 12 atoms
Calcium (Ca) 6 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. (pdb code 2ox8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain., PDB code: 2ox8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 2ox8

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Zinc binding site 1 out of 16 in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1

b:19.4
occ:1.00
CL A:CL6 2.0 39.5 1.0
NE2 A:HIS610 2.2 19.5 1.0
CL A:CL7 2.3 18.2 1.0
CD2 A:HIS610 3.1 17.9 1.0
CE1 A:HIS610 3.2 22.1 1.0
CG A:HIS610 4.3 18.5 1.0
ND1 A:HIS610 4.3 19.4 1.0

Zinc binding site 2 out of 16 in 2ox8

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Zinc binding site 2 out of 16 in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn2

b:22.9
occ:1.00
OE2 A:GLU731 1.9 26.5 1.0
OE1 A:GLU650 2.0 14.9 1.0
CL A:CL8 2.1 37.7 1.0
O A:PHE644 2.1 11.4 1.0
CD A:GLU731 2.8 26.3 1.0
CD A:GLU650 2.8 14.8 1.0
OE2 A:GLU650 3.0 15.2 1.0
OE1 A:GLU731 3.1 28.4 1.0
C A:PHE644 3.3 12.5 1.0
OH A:TYR619 3.6 16.0 1.0
N A:PHE644 4.0 8.5 1.0
CA A:PHE644 4.1 9.9 1.0
CD A:LYS617 4.1 20.2 1.0
CB A:PHE644 4.1 7.0 1.0
CG A:GLU731 4.2 24.9 1.0
CE A:LYS617 4.2 15.8 1.0
N A:ILE645 4.2 14.7 1.0
CG A:GLU650 4.3 14.7 1.0
CG2 A:VAL643 4.3 7.7 1.0
CA A:ILE645 4.4 17.6 1.0
CE2 A:TYR619 4.4 16.2 1.0
CZ A:TYR619 4.5 17.1 1.0
N A:ASN646 4.7 18.2 1.0
ND2 A:ASN646 4.9 27.8 1.0

Zinc binding site 3 out of 16 in 2ox8

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Zinc binding site 3 out of 16 in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3

b:32.2
occ:1.00
OD2 A:ASP733 1.8 16.2 1.0
OD2 A:ASP616 1.9 18.9 1.0
CG A:ASP616 2.7 19.8 1.0
O A:HOH743 2.8 24.3 1.0
OD1 A:ASP616 2.9 19.0 1.0
CG A:ASP733 3.0 17.9 1.0
OD1 A:ASP733 3.6 21.2 1.0
NZ A:LYS617 3.6 21.4 1.0
CB A:ASP616 4.1 17.8 1.0
CB A:ASP733 4.2 16.7 1.0
CE A:LYS617 4.6 15.8 1.0

Zinc binding site 4 out of 16 in 2ox8

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Zinc binding site 4 out of 16 in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn4

b:34.4
occ:1.00
OD1 A:ASP707 1.8 17.4 1.0
OD2 A:ASP670 2.0 27.4 1.0
OD1 A:ASP670 2.1 25.4 1.0
NE2 A:HIS702 2.2 26.5 1.0
CG A:ASP670 2.4 28.4 1.0
OE1 A:GLU674 2.4 54.4 1.0
OE2 A:GLU674 2.6 57.7 1.0
CD A:GLU674 2.8 56.1 1.0
CG A:ASP707 2.8 29.5 1.0
CD2 A:HIS702 3.1 29.8 1.0
CE1 A:HIS702 3.2 30.2 1.0
CB A:ASP707 3.4 33.9 1.0
O A:HOH754 3.5 40.5 1.0
CA A:ASP707 3.8 38.0 1.0
CB A:ASP670 3.9 29.1 1.0
OD2 A:ASP707 3.9 29.4 1.0
O A:GLU706 4.1 41.0 1.0
CG A:GLU674 4.3 55.4 1.0
ND1 A:HIS702 4.3 30.5 1.0
CG A:HIS702 4.3 32.2 1.0
CZ2 A:TRP677 4.4 17.8 1.0
N A:ASP707 4.5 40.8 1.0
C A:ASP670 4.5 33.4 1.0
C A:GLU706 4.6 42.6 1.0
O A:ASP670 4.6 34.7 1.0
N A:ASN675 4.6 47.2 1.0
CA A:GLU674 4.7 49.8 1.0
CA A:ASP670 4.7 30.1 1.0
CB A:GLU674 4.9 51.5 1.0
N A:SER671 4.9 36.7 1.0
CE2 A:TRP677 5.0 19.4 1.0
C A:ASP707 5.0 38.9 1.0

Zinc binding site 5 out of 16 in 2ox8

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Zinc binding site 5 out of 16 in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn5

b:34.9
occ:1.00
OE1 A:GLU662 1.7 39.4 1.0
NE2 A:HIS664 2.0 24.5 1.0
O A:HOH744 2.4 11.1 1.0
O A:HOH746 2.4 18.4 1.0
CD A:GLU662 2.7 38.0 1.0
CE1 A:HIS664 2.8 23.1 1.0
OE2 A:GLU662 3.0 36.9 1.0
CD2 A:HIS664 3.2 22.4 1.0
O A:GLY660 3.8 43.1 1.0
ND1 A:HIS664 3.9 24.1 1.0
CG A:GLU662 4.1 37.8 1.0
CG A:HIS664 4.2 23.6 1.0
O A:GLU662 4.2 35.4 1.0
C A:GLY660 4.3 43.4 1.0
N A:GLY660 4.4 42.8 1.0
CA A:GLY660 4.4 42.5 1.0
CG A:MET658 4.5 41.9 1.0
CB A:GLU662 4.6 37.4 1.0
CA A:MET658 4.7 40.0 1.0
CB A:MET658 4.7 40.1 1.0
CD2 A:PHE621 4.7 10.8 1.0
CE A:MET658 4.7 45.5 1.0
N A:GLU662 4.8 40.2 1.0
N A:VAL659 4.9 43.0 1.0
C A:GLU662 5.0 34.9 1.0

Zinc binding site 6 out of 16 in 2ox8

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Zinc binding site 6 out of 16 in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1

b:15.8
occ:1.00
NE2 B:HIS610 2.0 17.1 1.0
CL B:CL6 2.3 22.4 1.0
CL B:CL7 2.3 14.8 1.0
CE1 B:HIS610 2.7 18.0 1.0
CD2 B:HIS610 3.1 18.3 1.0
ND1 B:HIS610 3.8 16.4 1.0
CG B:HIS610 4.1 17.2 1.0

Zinc binding site 7 out of 16 in 2ox8

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Zinc binding site 7 out of 16 in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn2

b:25.1
occ:1.00
O B:PHE644 1.9 14.5 1.0
OE1 B:GLU650 1.9 23.2 1.0
CL B:CL8 2.0 34.0 1.0
OE1 B:GLU731 2.2 16.1 1.0
CD B:GLU650 2.8 24.0 1.0
CD B:GLU731 2.9 21.4 1.0
OE2 B:GLU731 3.0 21.2 1.0
C B:PHE644 3.0 17.4 1.0
OE2 B:GLU650 3.1 24.8 1.0
OH B:TYR619 3.8 17.9 1.0
N B:PHE644 3.8 14.2 1.0
CA B:PHE644 3.9 13.1 1.0
CB B:PHE644 4.0 10.4 1.0
N B:ILE645 4.0 17.9 1.0
CE B:LYS617 4.1 13.2 1.0
CA B:ILE645 4.2 18.6 1.0
CD B:LYS617 4.2 14.6 1.0
CG2 B:VAL643 4.2 12.2 1.0
CG B:GLU650 4.2 23.8 1.0
CG B:GLU731 4.4 17.9 1.0
CE2 B:TYR619 4.4 18.8 1.0
CZ B:TYR619 4.5 20.5 1.0
N B:ASN646 4.6 20.4 1.0
C B:ILE645 4.9 20.1 1.0
C B:VAL643 5.0 15.2 1.0

Zinc binding site 8 out of 16 in 2ox8

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Zinc binding site 8 out of 16 in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3

b:27.7
occ:1.00
OD2 B:ASP733 1.8 23.5 1.0
OD2 B:ASP616 1.9 21.8 1.0
NE2 A:HIS700 1.9 28.3 1.0
O A:HOH745 2.4 21.8 1.0
CG B:ASP616 2.7 22.8 1.0
CG B:ASP733 2.7 22.4 1.0
CD2 A:HIS700 2.8 27.3 1.0
OD1 B:ASP616 2.9 23.3 1.0
CE1 A:HIS700 3.0 30.1 1.0
OD1 B:ASP733 3.0 18.4 1.0
CG A:HIS700 4.0 28.7 1.0
ND1 A:HIS700 4.0 29.2 1.0
NZ B:LYS617 4.1 13.9 1.0
O B:HOH748 4.1 32.9 1.0
CB B:ASP733 4.1 17.7 1.0
CB B:ASP616 4.2 21.1 1.0
CB A:TRP698 4.2 28.2 1.0
O A:TRP698 4.2 28.8 1.0
O B:ASP616 5.0 22.8 1.0

Zinc binding site 9 out of 16 in 2ox8

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Zinc binding site 9 out of 16 in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn4

b:35.8
occ:1.00
OD1 B:ASP707 1.8 28.7 1.0
OD1 B:ASP670 2.1 35.5 1.0
OE2 B:GLU674 2.2 53.3 1.0
OD2 B:ASP670 2.2 31.9 1.0
NE2 B:HIS702 2.2 31.5 1.0
CG B:ASP670 2.4 33.2 1.0
OE1 B:GLU674 2.7 55.2 1.0
CD B:GLU674 2.7 53.0 1.0
CG B:ASP707 2.9 36.2 1.0
CD2 B:HIS702 3.1 30.4 1.0
CE1 B:HIS702 3.2 31.3 1.0
CB B:ASP707 3.4 38.4 1.0
CA B:ASP707 3.7 40.0 1.0
O B:GLU706 3.9 40.6 1.0
OD2 B:ASP707 3.9 36.2 1.0
CB B:ASP670 4.0 31.5 1.0
O B:ASP670 4.2 36.5 1.0
CG B:GLU674 4.2 52.3 1.0
CG B:HIS702 4.3 31.8 1.0
ND1 B:HIS702 4.3 30.5 1.0
CZ2 B:TRP677 4.4 30.4 1.0
N B:ASP707 4.4 40.7 1.0
C B:GLU706 4.4 41.8 1.0
C B:ASP670 4.4 34.5 1.0
N B:ASN675 4.6 49.9 1.0
CA B:ASP670 4.8 32.5 1.0
CA B:GLU674 4.8 49.9 1.0
CB B:GLU674 4.9 50.4 1.0
C B:ASP707 4.9 40.1 1.0
CE2 B:TRP677 4.9 32.0 1.0

Zinc binding site 10 out of 16 in 2ox8

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Zinc binding site 10 out of 16 in the Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Human Scavenger Receptor C-Type Lectin Carbohydrate- Recognition Domain. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn5

b:44.3
occ:1.00
OE1 B:GLU662 2.0 40.1 1.0
OE2 B:GLU662 2.2 39.1 1.0
NE2 B:HIS664 2.2 26.7 1.0
CD B:GLU662 2.3 37.8 1.0
O B:HOH743 2.5 22.9 1.0
CE1 B:HIS664 3.1 23.4 1.0
CD2 B:HIS664 3.2 23.8 1.0
CG B:GLU662 3.9 37.1 1.0
O B:GLY660 4.0 45.8 1.0
O B:GLU662 4.0 35.8 1.0
ND1 B:HIS664 4.2 23.9 1.0
CG B:HIS664 4.3 24.7 1.0
N B:GLY660 4.4 45.7 1.0
CA B:GLY660 4.4 44.6 1.0
C B:GLY660 4.4 44.9 1.0
CE B:MET658 4.5 46.6 1.0
CB B:GLU662 4.7 36.2 1.0
CG B:MET658 4.7 44.0 1.0
CA B:MET658 4.7 41.3 1.0
CB B:MET658 4.8 42.4 1.0
CD2 B:PHE621 4.8 9.4 1.0
N B:GLU662 4.8 38.8 1.0
C B:GLU662 4.9 36.2 1.0

Reference:

H.Feinberg, M.E.Taylor, W.I.Weis. Scavenger Receptor C-Type Lectin Binds to the Leukocyte Cell Surface Glycan Lewis(X) By A Novel Mechanism. J.Biol.Chem. V. 282 17250 2007.
ISSN: ISSN 0021-9258
PubMed: 17420244
DOI: 10.1074/JBC.M701624200
Page generated: Wed Dec 16 03:47:22 2020

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