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Zinc in PDB 2om1: Structure of Human Insulin in Presence of Thiocyanate at pH 6.5

Protein crystallography data

The structure of Structure of Human Insulin in Presence of Thiocyanate at pH 6.5, PDB code: 2om1 was solved by M.Norrman, G.Schluckebier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 1.97
Space group C 2 2 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.000, 219.480, 224.480, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human Insulin in Presence of Thiocyanate at pH 6.5 (pdb code 2om1). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Structure of Human Insulin in Presence of Thiocyanate at pH 6.5, PDB code: 2om1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 2om1

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Zinc binding site 1 out of 6 in the Structure of Human Insulin in Presence of Thiocyanate at pH 6.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Insulin in Presence of Thiocyanate at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:21.6
occ:1.00
 N B:SCN905 1.8 29.1 1.0
NE2 F:HIS10 1.9 23.1 1.0
NE2 B:HIS10 2.0 25.9 1.0
NE2 J:HIS10 2.0 26.2 1.0
CE1 F:HIS10 2.8 29.0 1.0
CE1 J:HIS10 2.9 29.1 1.0
CD2 B:HIS10 3.0 23.3 1.0
CE1 B:HIS10 3.0 28.5 1.0
C B:SCN905 3.0 29.8 1.0
CD2 F:HIS10 3.0 25.7 1.0
CD2 J:HIS10 3.1 25.0 1.0
ND1 F:HIS10 4.0 26.2 1.0
ND1 B:HIS10 4.1 25.0 1.0
ND1 J:HIS10 4.1 29.4 1.0
CG B:HIS10 4.1 23.7 1.0
CG F:HIS10 4.1 26.8 1.0
CG J:HIS10 4.2 27.8 1.0
O J:LEU6 4.6 30.2 1.0
O B:LEU6 4.7 25.8 1.0
O F:LEU6 4.7 28.6 1.0
CB F:LEU6 4.7 26.8 1.0
S B:SCN905 4.8 31.8 1.0
CB J:LEU6 4.8 29.8 1.0
CB B:LEU6 4.9 24.7 1.0
O B:HOH909 4.9 29.7 1.0

Zinc binding site 2 out of 6 in 2om1

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Zinc binding site 2 out of 6 in the Structure of Human Insulin in Presence of Thiocyanate at pH 6.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Insulin in Presence of Thiocyanate at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn802

b:19.9
occ:1.00
 N D:SCN906 1.8 18.2 1.0
NE2 D:HIS10 2.0 23.4 1.0
NE2 L:HIS10 2.0 22.9 1.0
NE2 H:HIS10 2.0 24.9 1.0
CE1 L:HIS10 2.9 24.5 1.0
CE1 D:HIS10 2.9 27.1 1.0
C D:SCN906 3.0 18.1 1.0
CE1 H:HIS10 3.0 25.2 1.0
CD2 D:HIS10 3.0 23.1 1.0
CD2 H:HIS10 3.0 25.0 1.0
CD2 L:HIS10 3.1 24.2 1.0
ND1 L:HIS10 4.0 25.6 1.0
ND1 D:HIS10 4.1 25.9 1.0
ND1 H:HIS10 4.1 25.8 1.0
O H:HOH46 4.1 38.9 1.0
CG D:HIS10 4.1 24.7 1.0
CG H:HIS10 4.2 24.7 1.0
CG L:HIS10 4.2 28.9 1.0
O D:LEU6 4.7 21.7 1.0
O L:LEU6 4.7 27.9 1.0
CB H:LEU6 4.7 24.9 1.0
S D:SCN906 4.7 22.0 1.0
O H:LEU6 4.8 25.2 1.0
CB D:LEU6 4.8 22.3 1.0
O H:HOH47 4.8 26.2 1.0
O L:HOH47 4.9 36.9 1.0
CB L:LEU6 4.9 27.1 1.0
O D:HOH917 4.9 34.5 1.0

Zinc binding site 3 out of 6 in 2om1

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Zinc binding site 3 out of 6 in the Structure of Human Insulin in Presence of Thiocyanate at pH 6.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human Insulin in Presence of Thiocyanate at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Zn803

b:19.5
occ:1.00
 N R:SCN903 1.9 21.6 1.0
NE2 V:HIS10 1.9 22.2 1.0
NE2 T:HIS10 2.0 19.6 1.0
NE2 R:HIS10 2.0 23.7 1.0
CE1 T:HIS10 2.8 26.0 1.0
CE1 V:HIS10 2.9 24.9 1.0
CE1 R:HIS10 3.0 26.5 1.0
CD2 V:HIS10 3.0 21.8 1.0
C R:SCN903 3.0 22.2 1.0
CD2 T:HIS10 3.1 23.1 1.0
CD2 R:HIS10 3.1 25.6 1.0
ND1 T:HIS10 4.0 25.1 1.0
ND1 V:HIS10 4.0 23.4 1.0
ND1 R:HIS10 4.1 26.1 1.0
CG V:HIS10 4.1 23.7 1.0
CG T:HIS10 4.1 23.6 1.0
CG R:HIS10 4.2 26.5 1.0
O R:HOH923 4.3 45.8 1.0
CB R:LEU6 4.6 23.4 1.0
CB V:LEU6 4.6 24.3 1.0
O R:LEU6 4.7 22.5 1.0
O V:LEU6 4.8 24.9 1.0
CB T:LEU6 4.8 23.4 1.0
S R:SCN903 4.8 23.7 1.0
O T:LEU6 4.9 24.0 1.0
O T:HOH1107 4.9 28.3 1.0
O R:HOH928 5.0 31.6 1.0

Zinc binding site 4 out of 6 in 2om1

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Zinc binding site 4 out of 6 in the Structure of Human Insulin in Presence of Thiocyanate at pH 6.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human Insulin in Presence of Thiocyanate at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Zn804

b:21.9
occ:1.00
 N Y:SCN904 1.8 23.9 1.0
NE2 2:HIS10 2.0 24.7 1.0
NE2 Y:HIS10 2.0 23.0 1.0
NE2 4:HIS10 2.0 23.6 1.0
CE1 4:HIS10 2.9 29.2 1.0
CE1 2:HIS10 2.9 28.7 1.0
CE1 Y:HIS10 3.0 27.9 1.0
C Y:SCN904 3.0 25.2 1.0
CD2 2:HIS10 3.0 25.2 1.0
CD2 Y:HIS10 3.1 22.6 1.0
CD2 4:HIS10 3.1 26.2 1.0
ND1 4:HIS10 4.1 27.5 1.0
ND1 2:HIS10 4.1 28.4 1.0
ND1 Y:HIS10 4.1 28.1 1.0
CG 2:HIS10 4.2 27.4 1.0
CG Y:HIS10 4.2 25.6 1.0
CG 4:HIS10 4.2 27.9 1.0
O Y:LEU6 4.6 24.9 1.0
O 2:LEU6 4.7 28.4 1.0
O 4:LEU6 4.7 26.2 1.0
S Y:SCN904 4.7 29.9 1.0
CB 2:LEU6 4.8 27.9 1.0
O Y:HOH915 4.8 32.2 1.0
O 2:HOH41 4.9 27.7 1.0
CB 4:LEU6 4.9 26.8 1.0
CB Y:LEU6 4.9 26.7 1.0
O 4:HOH32 4.9 35.4 1.0
CG Y:LEU6 4.9 29.8 1.0

Zinc binding site 5 out of 6 in 2om1

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Zinc binding site 5 out of 6 in the Structure of Human Insulin in Presence of Thiocyanate at pH 6.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Human Insulin in Presence of Thiocyanate at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Zn806

b:24.1
occ:1.00
 N b:SCN901 1.8 26.8 1.0
NE2 d:HIS10 2.0 26.1 1.0
NE2 f:HIS10 2.0 28.4 1.0
NE2 b:HIS10 2.1 27.8 1.0
CE1 f:HIS10 3.0 31.2 1.0
CE1 d:HIS10 3.0 27.0 1.0
C b:SCN901 3.0 27.4 1.0
CD2 b:HIS10 3.0 26.6 1.0
CD2 d:HIS10 3.0 23.6 1.0
CD2 f:HIS10 3.1 27.1 1.0
CE1 b:HIS10 3.1 28.5 1.0
O f:HOH39 4.1 39.1 1.0
ND1 d:HIS10 4.1 27.0 1.0
ND1 f:HIS10 4.1 29.0 1.0
CG d:HIS10 4.2 26.3 1.0
ND1 b:HIS10 4.2 31.2 1.0
CG b:HIS10 4.2 30.7 1.0
CG f:HIS10 4.2 30.0 1.0
O f:LEU6 4.6 29.9 1.0
O b:LEU6 4.7 31.0 1.0
O d:LEU6 4.8 28.4 1.0
S b:SCN901 4.8 32.0 1.0
CB d:LEU6 4.8 28.5 1.0
CB b:LEU6 4.8 31.1 1.0
CB f:LEU6 4.9 31.1 1.0
O d:HOH42 4.9 34.5 1.0
O f:HOH38 4.9 37.6 1.0

Zinc binding site 6 out of 6 in 2om1

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Zinc binding site 6 out of 6 in the Structure of Human Insulin in Presence of Thiocyanate at pH 6.5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Human Insulin in Presence of Thiocyanate at pH 6.5 within 5.0Å range:
probe atom residue distance (Å) B Occ
h:Zn805

b:26.3
occ:1.00
 N h:SCN902 1.7 29.3 1.0
NE2 l:HIS10 2.0 30.8 1.0
NE2 h:HIS10 2.0 26.1 1.0
NE2 j:HIS10 2.1 30.3 1.0
CE1 j:HIS10 2.9 29.3 1.0
CE1 l:HIS10 2.9 34.1 1.0
C h:SCN902 2.9 30.3 1.0
CD2 h:HIS10 2.9 24.8 1.0
CE1 h:HIS10 3.1 28.4 1.0
CD2 l:HIS10 3.1 33.0 1.0
CD2 j:HIS10 3.2 28.7 1.0
ND1 l:HIS10 4.0 33.2 1.0
ND1 j:HIS10 4.1 30.2 1.0
CG h:HIS10 4.1 25.4 1.0
ND1 h:HIS10 4.1 25.4 1.0
CG l:HIS10 4.2 33.0 1.0
CG j:HIS10 4.2 29.6 1.0
O h:LEU6 4.6 27.3 1.0
O j:LEU6 4.7 35.3 1.0
S h:SCN902 4.7 32.7 1.0
CB h:LEU6 4.7 28.6 1.0
O l:LEU6 4.7 36.2 1.0
CB j:LEU6 4.8 35.8 1.0
CB l:LEU6 4.8 34.0 1.0
O h:HOH909 4.9 33.9 1.0
O l:HOH31 5.0 35.7 1.0

Reference:

M.Norrman, G.Schluckebier. Crystallographic Characterization of Two Novel Crystal Forms of Human Insulin Induced By Chaotropic Agents and A Shift in pH. Bmc Struct.Biol. V. 7 83 2007.
ISSN: ESSN 1472-6807
PubMed: 18093308
DOI: 10.1186/1472-6807-7-83
Page generated: Wed Dec 16 03:46:17 2020

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