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Platinum in PDB 6ig4: Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74

Enzymatic activity of Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74

All present enzymatic activity of Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74:
2.7.7.41;

Protein crystallography data

The structure of Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74, PDB code: 6ig4 was solved by H.Z.Jiao, Y.Yin, Z.F.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.68 / 2.26
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 109.069, 116.538, 108.548, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22

Platinum Binding Sites:

The binding sites of Platinum atom in the Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74 (pdb code 6ig4). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 10 binding sites of Platinum where determined in the Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74, PDB code: 6ig4:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Platinum binding site 1 out of 10 in 6ig4

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Platinum binding site 1 out of 10 in the Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt401

b:50.0
occ:1.00
 PT A:3G0401 0.0 50.0 1.0
C2 A:3G0401 1.9 13.4 1.0
C3 A:3G0401 2.0 39.7 1.0
C4 A:3G0401 2.0 34.6 1.0
C1 A:3G0401 2.0 54.4 1.0
N3 A:3G0401 3.1 25.4 1.0
N2 A:3G0401 3.1 36.0 1.0
N1 A:3G0401 3.2 28.1 1.0
N4 A:3G0401 3.2 37.1 1.0
OE1 A:GLN254 3.7 35.9 1.0
NE2 A:GLN254 4.0 31.8 1.0
CD A:GLN254 4.0 34.9 1.0
CZ A:PHE240 4.5 33.9 1.0
CA A:GLY79 4.7 29.2 1.0

Platinum binding site 2 out of 10 in 6ig4

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Platinum binding site 2 out of 10 in the Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt402

b:58.3
occ:0.44
 PT A:3G0402 0.0 58.3 0.4
C2 A:3G0402 2.0 34.4 0.4
C1 A:3G0402 2.0 40.0 0.4
C3 A:3G0402 2.0 39.3 0.4
C4 A:3G0402 2.0 37.9 0.4
N2 A:3G0402 3.2 40.2 0.4
N3 A:3G0402 3.2 30.4 0.4
N1 A:3G0402 3.2 32.8 0.4
N4 A:3G0402 3.2 24.0 0.4
CG A:GLN114 3.9 41.7 1.0
CB A:GLN114 4.4 21.2 1.0
CD A:GLN114 4.4 44.7 1.0
OE1 A:GLN114 4.6 39.8 1.0

Platinum binding site 3 out of 10 in 6ig4

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Platinum binding site 3 out of 10 in the Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt403

b:79.7
occ:1.00
 CG A:LYS110 3.9 35.1 1.0
NZ A:LYS110 4.1 60.0 1.0
CG1 A:VAL106 4.2 31.3 1.0
CB A:LYS110 4.8 31.3 1.0
CD A:LYS110 4.8 51.3 1.0
PT A:PT404 4.8 97.0 1.0
CA A:LYS107 4.9 29.2 1.0
CE A:LYS110 5.0 55.6 1.0

Platinum binding site 4 out of 10 in 6ig4

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Platinum binding site 4 out of 10 in the Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt404

b:97.0
occ:1.00
 N3 A:3G0402 3.5 30.4 0.4
CG A:LYS107 4.2 51.6 1.0
CB A:LYS110 4.4 31.3 1.0
C3 A:3G0402 4.5 39.3 0.4
CD A:LYS107 4.7 66.6 1.0
CG1 A:ILE111 4.7 25.8 1.0
PT A:PT403 4.8 79.7 1.0

Platinum binding site 5 out of 10 in 6ig4

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Platinum binding site 5 out of 10 in the Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt405

b:0.4
occ:1.00
 OD2 A:ASP104 3.3 54.7 1.0
CD A:LYS107 4.2 66.6 1.0
CB A:LYS107 4.3 33.7 1.0
CG A:ASP104 4.3 46.2 1.0
CG A:LYS107 4.7 51.6 1.0
CE A:LYS107 4.7 66.5 1.0
CB A:ASP104 4.7 41.0 1.0

Platinum binding site 6 out of 10 in 6ig4

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Platinum binding site 6 out of 10 in the Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt406

b:0.1
occ:1.00
 CB A:PRO286 4.7 33.8 1.0
N A:CYS33 4.8 65.1 1.0
CB A:ALA256 4.8 23.4 1.0
CG A:PRO286 4.8 36.7 1.0

Platinum binding site 7 out of 10 in 6ig4

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Platinum binding site 7 out of 10 in the Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 7 of Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt407

b:98.7
occ:1.00
 OD1 A:ASP285 2.4 49.9 1.0
CG A:ASP285 3.3 44.0 1.0
OD2 A:ASP285 3.5 56.6 1.0
OG A:SER287 3.5 49.6 1.0
N A:CYS33 3.7 65.1 1.0
O A:HOH600 4.1 44.6 1.0
CB A:SER287 4.1 36.6 1.0
CD A:PRO286 4.3 39.7 1.0
N A:SER287 4.4 36.4 1.0
CB A:ASP285 4.7 43.5 1.0
CA A:CYS33 4.7 57.0 1.0
N A:PRO286 4.8 34.0 1.0
O A:CYS33 4.8 46.6 1.0
CA A:SER287 4.9 31.2 1.0

Platinum binding site 8 out of 10 in 6ig4

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Platinum binding site 8 out of 10 in the Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 8 of Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt401

b:59.3
occ:1.00
 PT B:3G0401 0.0 59.3 1.0
C1 B:3G0401 2.0 41.3 1.0
C4 B:3G0401 2.0 24.6 1.0
C2 B:3G0401 2.0 22.2 1.0
C3 B:3G0401 2.0 55.9 1.0
N1 B:3G0401 3.1 26.0 1.0
N4 B:3G0401 3.2 37.4 1.0
N2 B:3G0401 3.2 35.5 1.0
N3 B:3G0401 3.2 28.9 1.0
OE1 B:GLN254 3.5 39.2 1.0
CD B:GLN254 4.0 39.9 1.0
NE2 B:GLN254 4.2 39.4 1.0
CZ B:PHE240 4.4 47.0 1.0
NE B:ARG245 4.8 64.7 1.0
CG2 B:ILE250 4.8 23.5 1.0
CA B:GLY79 4.9 35.2 1.0
CE1 B:PHE240 4.9 44.7 1.0
CD B:ARG245 4.9 49.9 1.0

Platinum binding site 9 out of 10 in 6ig4

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Platinum binding site 9 out of 10 in the Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 9 of Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt402

b:54.5
occ:0.50
 OD1 B:ASN125 4.2 49.9 1.0
CA B:PHE122 5.0 72.1 1.0

Platinum binding site 10 out of 10 in 6ig4

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Platinum binding site 10 out of 10 in the Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 10 of Structure of Mitochondrial Cdp-Dag Synthase TAM41, Delta 74 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt403

b:88.3
occ:1.00
 NE2 B:HIS273 2.6 49.8 1.0
O B:HOH583 3.2 57.5 1.0
CE1 B:HIS273 3.3 47.5 1.0
O B:HOH598 3.4 44.7 1.0
CG B:HIS296 3.4 31.2 1.0
CD2 B:HIS296 3.6 43.9 1.0
CB B:HIS296 3.7 32.6 1.0
CD2 B:HIS273 3.8 40.2 1.0
ND1 B:HIS296 3.9 46.8 1.0
NE2 B:HIS296 4.1 47.2 1.0
NH2 B:ARG216 4.2 49.3 1.0
CE1 B:HIS296 4.3 37.8 1.0
ND1 B:HIS273 4.5 45.0 1.0
CG B:HIS273 4.8 34.6 1.0

Reference:

H.Jiao, Y.Yin, Z.Liu. Structures of the Mitochondrial Cdp-Dag Synthase TAM41 Suggest A Potential Lipid Substrate Pathway From Membrane to the Active Site. Structure V. 27 1258 2019.
ISSN: ISSN 0969-2126
PubMed: 31178220
DOI: 10.1016/J.STR.2019.04.017
Page generated: Thu Oct 10 11:45:38 2024

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