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Zinc in PDB 2cb8: High Resolution Crystal Structure of Liganded Human L-Acbp

Protein crystallography data

The structure of High Resolution Crystal Structure of Liganded Human L-Acbp, PDB code: 2cb8 was solved by J.P.Taskinen, D.M.Van Aalten, J.Knudsen, R.K.Wierenga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.29 / 1.4
Space group I 2 3
Cell size a, b, c (Å), α, β, γ (°) 118.490, 118.490, 118.490, 90.00, 90.00, 90.00
R / Rfree (%) 17.1 / 19.4

Zinc Binding Sites:

The binding sites of Zinc atom in the High Resolution Crystal Structure of Liganded Human L-Acbp (pdb code 2cb8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the High Resolution Crystal Structure of Liganded Human L-Acbp, PDB code: 2cb8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2cb8

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Zinc binding site 1 out of 8 in the High Resolution Crystal Structure of Liganded Human L-Acbp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of High Resolution Crystal Structure of Liganded Human L-Acbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1089

b:26.0
occ:1.00
O A:HOH2151 2.0 25.5 1.0
NE2 A:HIS31 2.2 14.9 1.0
O A:HOH2150 2.2 25.1 1.0
OE2 B:GLU7 2.2 19.9 1.0
OE1 B:GLU7 2.3 24.7 1.0
CD B:GLU7 2.6 19.2 1.0
CE1 A:HIS31 3.1 13.5 1.0
CD2 A:HIS31 3.1 12.4 1.0
O B:HOH2016 3.9 41.8 1.0
O A:HOH2052 3.9 38.4 1.0
CD2 A:LEU62 4.0 16.5 1.0
O B:HOH2020 4.0 41.8 1.0
CG B:GLU7 4.1 19.3 1.0
ND1 A:HIS31 4.2 12.5 1.0
CB A:ALA73 4.2 13.2 1.0
CG A:HIS31 4.2 10.3 1.0
O B:HOH2019 4.3 42.3 1.0
CZ A:PHE27 4.4 14.6 1.0
CE2 A:PHE27 4.4 13.7 1.0
CB B:GLU7 4.9 17.9 1.0
CD1 A:LEU62 5.0 14.2 1.0

Zinc binding site 2 out of 8 in 2cb8

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Zinc binding site 2 out of 8 in the High Resolution Crystal Structure of Liganded Human L-Acbp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of High Resolution Crystal Structure of Liganded Human L-Acbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1090

b:20.3
occ:1.00
O7A A:MYA1094 1.8 22.7 1.0
O4 A:SO41095 2.0 24.1 0.3
O2A A:MYA1088 2.1 27.8 1.0
S A:SO41095 3.2 22.4 0.3
P3X A:MYA1094 3.2 21.0 1.0
P1A A:MYA1088 3.4 27.9 1.0
O1 A:SO41095 3.5 22.8 0.3
O3 A:SO41095 3.6 18.6 0.3
O8A A:MYA1094 3.8 26.9 1.0
O1A A:MYA1088 3.8 28.1 1.0
ZN A:ZN1096 3.9 17.1 0.3
NH2 A:ARG14 3.9 18.6 0.5
O3X A:MYA1094 4.2 21.8 1.0
O9A A:MYA1094 4.2 25.3 1.0
C4X A:MYA1094 4.3 21.5 1.0
C5X A:MYA1094 4.3 21.2 1.0
NH1 A:ARG14 4.3 12.7 0.5
O3A A:MYA1088 4.3 29.3 1.0
C3X A:MYA1094 4.3 20.7 1.0
C5X A:MYA1088 4.4 25.4 1.0
O2 A:SO41095 4.4 21.4 0.3
ZN A:ZN1093 4.4 19.7 0.7
O5X A:MYA1088 4.4 26.5 1.0
CAM B:MYA1088 4.5 32.0 1.0
C9M B:MYA1088 4.5 31.4 1.0

Zinc binding site 3 out of 8 in 2cb8

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Zinc binding site 3 out of 8 in the High Resolution Crystal Structure of Liganded Human L-Acbp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of High Resolution Crystal Structure of Liganded Human L-Acbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1091

b:19.9
occ:1.00
OD2 A:ASP22 1.9 13.3 1.0
N1A A:MYA1094 2.0 19.1 1.0
CG A:ASP22 2.6 12.8 1.0
OD1 A:ASP22 2.7 12.8 1.0
C2A A:MYA1094 2.8 21.5 1.0
C6A A:MYA1094 3.0 18.5 1.0
N6A A:MYA1094 3.2 18.3 1.0
CB A:ASP22 4.1 11.8 1.0
N3A A:MYA1094 4.1 19.0 1.0
O A:HOH2049 4.3 34.4 1.0
C5A A:MYA1094 4.3 19.1 1.0
O2M B:MYA1088 4.6 47.7 1.0
C3 B:MYA1088 4.7 37.6 1.0
C4A A:MYA1094 4.7 18.2 1.0
O A:HOH2050 4.9 28.9 1.0
C2M B:MYA1088 4.9 39.5 1.0
O A:HOH2047 5.0 27.2 1.0

Zinc binding site 4 out of 8 in 2cb8

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Zinc binding site 4 out of 8 in the High Resolution Crystal Structure of Liganded Human L-Acbp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of High Resolution Crystal Structure of Liganded Human L-Acbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1092

b:42.3
occ:0.70
OE2 A:GLU68 2.5 33.7 1.0
O A:HOH2152 2.6 44.0 1.0
CD A:GLU68 3.2 30.5 1.0
N A:SER2 3.3 18.6 1.0
CA A:SER2 3.6 16.4 1.0
OE1 A:GLU68 3.7 31.2 1.0
O A:HOH2118 3.8 65.8 1.0
CE A:MET71 4.0 26.9 0.5
CG A:GLU68 4.2 23.9 1.0
CE A:LYS72 4.3 19.5 1.0
C A:SER2 4.6 14.7 1.0
CB A:SER2 4.6 16.8 1.0
CG A:LYS72 4.8 12.7 1.0
O A:HOH2005 4.9 37.9 1.0

Zinc binding site 5 out of 8 in 2cb8

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Zinc binding site 5 out of 8 in the High Resolution Crystal Structure of Liganded Human L-Acbp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of High Resolution Crystal Structure of Liganded Human L-Acbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1093

b:19.7
occ:0.70
O2A A:MYA1094 1.9 23.3 1.0
O3A A:MYA1088 1.9 29.3 1.0
O1 A:SO41095 1.9 22.8 0.3
P1A A:MYA1088 3.0 27.9 1.0
P1A A:MYA1094 3.2 20.5 1.0
S A:SO41095 3.3 22.4 0.3
O2A A:MYA1088 3.4 27.8 1.0
O1A A:MYA1088 3.4 28.1 1.0
O3A A:MYA1094 3.6 24.2 1.0
O3 A:SO41095 3.8 18.6 0.3
C5X A:MYA1094 3.8 21.2 1.0
O A:HOH2106 3.8 30.6 1.0
O5X A:MYA1094 4.0 20.5 1.0
O4 A:SO41095 4.0 24.1 0.3
O2 A:SO41095 4.2 21.4 0.3
O5X A:MYA1088 4.3 26.5 1.0
O1A A:MYA1094 4.3 26.6 1.0
ZN A:ZN1090 4.4 20.3 1.0
O A:HOH2001 4.7 51.9 1.0
O A:HOH2143 4.8 51.8 1.0
O A:HOH2153 4.8 35.4 1.0

Zinc binding site 6 out of 8 in 2cb8

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Zinc binding site 6 out of 8 in the High Resolution Crystal Structure of Liganded Human L-Acbp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of High Resolution Crystal Structure of Liganded Human L-Acbp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1096

b:17.1
occ:0.33
O8A A:MYA1094 2.0 26.9 1.0
O3 A:SO41095 2.2 18.6 0.3
S A:SO41095 3.0 22.4 0.3
O4 A:SO41095 3.0 24.1 0.3
P3X A:MYA1094 3.2 21.0 1.0
O7A A:MYA1094 3.6 22.7 1.0
O A:HOH2155 3.6 39.1 1.0
O2 A:SO41095 3.6 21.4 0.3
ZN A:ZN1090 3.9 20.3 1.0
O9A A:MYA1094 4.1 25.3 1.0
O3X A:MYA1094 4.1 21.8 1.0
O1 A:SO41095 4.2 22.8 0.3
O A:HOH2003 4.3 37.1 0.3
C3X A:MYA1094 4.3 20.7 1.0
O3A A:MYA1094 5.0 24.2 1.0

Zinc binding site 7 out of 8 in 2cb8

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Zinc binding site 7 out of 8 in the High Resolution Crystal Structure of Liganded Human L-Acbp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of High Resolution Crystal Structure of Liganded Human L-Acbp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1090

b:26.1
occ:1.00
OE2 A:GLU23 1.9 17.4 1.0
NE2 B:HIS15 2.0 12.0 1.0
OE2 B:GLU11 2.0 14.1 1.0
O B:HOH2131 2.2 31.1 1.0
O B:HOH2132 2.3 24.9 1.0
OE1 A:GLU23 2.4 18.1 1.0
CD A:GLU23 2.5 18.3 1.0
CD2 B:HIS15 3.0 12.0 1.0
CE1 B:HIS15 3.0 13.8 1.0
CD B:GLU11 3.1 13.2 1.0
CG B:GLU11 3.5 12.6 1.0
CG A:GLU23 3.9 16.7 1.0
O B:GLU11 4.0 10.9 1.0
ND1 B:HIS15 4.1 13.7 1.0
CG B:HIS15 4.1 10.3 1.0
OE1 B:GLU11 4.1 16.2 1.0
O A:HOH2056 4.2 32.0 1.0
O B:HOH2025 4.2 50.9 1.0
O A:HOH2055 4.3 29.9 1.0
O A:HOH2057 4.3 30.4 1.0
O A:HOH2058 4.5 53.0 1.0
C B:GLU11 4.7 10.1 1.0
CB B:GLU11 4.8 11.9 1.0
O A:HOH2059 4.8 34.5 1.0
O B:HOH2026 4.9 50.3 1.0
CB A:GLU23 4.9 14.0 1.0
CA B:GLU11 5.0 10.7 1.0

Zinc binding site 8 out of 8 in 2cb8

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Zinc binding site 8 out of 8 in the High Resolution Crystal Structure of Liganded Human L-Acbp


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of High Resolution Crystal Structure of Liganded Human L-Acbp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1091

b:26.1
occ:1.00
O5A B:MYA1088 1.9 31.4 1.0
O2A B:MYA1088 2.0 28.7 1.0
O B:HOH2133 2.0 26.4 1.0
O B:HOH2134 2.1 27.2 1.0
P2A B:MYA1088 3.1 27.2 1.0
P1A B:MYA1088 3.3 26.9 1.0
O3A B:MYA1088 3.5 25.9 1.0
O6A B:MYA1088 3.7 33.7 1.0
O B:HOH2128 3.7 46.5 1.0
NZ A:LYS53 3.9 10.8 0.5
O A:HOH2104 4.0 34.9 1.0
O7A B:MYA1088 4.1 20.8 1.0
O B:HOH2122 4.1 39.3 1.0
C5X B:MYA1088 4.1 25.7 1.0
O5X B:MYA1088 4.2 26.8 1.0
NZ A:LYS53 4.2 19.4 0.5
O A:HOH2103 4.3 43.7 1.0
O4A B:MYA1088 4.4 30.0 1.0
O1A B:MYA1088 4.5 29.5 1.0
CE A:LYS53 4.6 9.8 0.5
O B:HOH2088 4.6 39.2 1.0
NZ B:LYS55 4.6 14.4 1.0
CE A:LYS53 4.7 18.3 0.5

Reference:

J.P.Taskinen, D.M.Van Aalten, J.Knudsen, R.K.Wierenga. High Resolution Crystal Structures of Unliganded and Liganded Human Liver Acbp Reveal A New Mode of Binding For the Acyl-Coa Ligand. Proteins: Struct., Funct., V. 66 229 2007BIOINF..
ISSN: ISSN 0887-3585
PubMed: 17044054
DOI: 10.1002/PROT.21124
Page generated: Wed Dec 16 03:19:08 2020

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