Zinc in PDB 7lt9: Crystal Structure of Ras Suppressor-1 in Complex with Pinch-1 LIM4-5 Domains

Protein crystallography data

The structure of Crystal Structure of Ras Suppressor-1 in Complex with Pinch-1 LIM4-5 Domains, PDB code: 7lt9 was solved by K.Fukuda, J.Qin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.57 / 3.05
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 51.042, 144.384, 185.691, 90, 90, 90
R / Rfree (%) 20 / 23.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Ras Suppressor-1 in Complex with Pinch-1 LIM4-5 Domains (pdb code 7lt9). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Ras Suppressor-1 in Complex with Pinch-1 LIM4-5 Domains, PDB code: 7lt9:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 7lt9

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Zinc binding site 1 out of 4 in the Crystal Structure of Ras Suppressor-1 in Complex with Pinch-1 LIM4-5 Domains


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 Ras Suppressor-1 in Complex with Pinch-1 LIM4-5 Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:62.6
occ:1.00
SG B:CYS278 2.1 59.0 1.0
SG B:CYS281 2.1 61.1 1.0
SG B:CYS300 2.3 61.3 1.0
SG B:CYS303 2.3 52.5 1.0
CB B:CYS278 3.2 65.5 1.0
CB B:CYS303 3.2 52.0 1.0
CB B:CYS281 3.3 58.4 1.0
CB B:CYS300 3.4 55.1 1.0
N B:CYS281 3.6 57.6 1.0
OG1 B:THR280 3.6 55.4 1.0
CA B:CYS281 4.0 58.5 1.0
N B:CYS300 4.1 55.2 1.0
CA B:CYS300 4.3 57.6 1.0
CA B:CYS303 4.4 60.3 1.0
C B:THR280 4.4 51.2 1.0
N B:CYS303 4.4 66.7 1.0
OG1 B:THR283 4.5 62.7 1.0
CA B:CYS278 4.6 64.2 1.0
C B:CYS281 4.7 61.2 1.0
CB B:THR280 4.8 49.7 1.0
O B:CYS300 4.8 62.4 1.0
N B:THR280 4.9 53.4 1.0
C B:CYS300 4.9 60.8 1.0
CA B:THR280 4.9 49.9 1.0
N B:ASN282 5.0 62.1 1.0

Zinc binding site 2 out of 4 in 7lt9

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Zinc binding site 2 out of 4 in the Crystal Structure of Ras Suppressor-1 in Complex with Pinch-1 LIM4-5 Domains


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 Ras Suppressor-1 in Complex with Pinch-1 LIM4-5 Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:76.8
occ:1.00
SG B:CYS275 2.2 70.1 1.0
SG B:CYS252 2.3 71.5 1.0
SG B:CYS255 2.3 87.6 1.0
SG B:CYS272 2.6 94.5 1.0
CB B:CYS252 2.9 66.4 1.0
CB B:CYS275 3.0 78.8 1.0
CB B:CYS272 3.3 78.8 1.0
CB B:CYS255 3.7 66.8 1.0
N B:CYS255 4.0 71.7 1.0
N B:CYS272 4.1 82.5 1.0
CA B:CYS272 4.3 79.6 1.0
CA B:CYS252 4.4 70.1 1.0
CA B:CYS255 4.4 67.2 1.0
CA B:CYS275 4.5 80.6 1.0
O B:CYS252 4.8 73.4 1.0
N B:CYS275 4.8 80.7 1.0
CB B:HIS254 4.9 63.9 1.0
C B:CYS252 4.9 75.2 1.0

Zinc binding site 3 out of 4 in 7lt9

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Zinc binding site 3 out of 4 in the Crystal Structure of Ras Suppressor-1 in Complex with Pinch-1 LIM4-5 Domains


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 Ras Suppressor-1 in Complex with Pinch-1 LIM4-5 Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:93.0
occ:1.00
ND1 B:HIS216 2.0 103.8 1.0
ND1 B:HIS213 2.2 102.4 1.0
SG B:CYS193 2.4 81.8 1.0
SG B:CYS196 2.6 101.8 1.0
CE1 B:HIS216 2.8 104.0 1.0
CG B:HIS216 3.0 113.5 1.0
CG B:HIS213 3.1 105.1 1.0
CE1 B:HIS213 3.2 99.6 1.0
CB B:CYS193 3.3 85.9 1.0
CB B:HIS213 3.4 114.8 1.0
CB B:HIS216 3.5 123.7 1.0
CB B:CYS196 3.5 91.1 1.0
NE2 B:HIS216 3.9 109.2 1.0
CD2 B:HIS216 3.9 110.4 1.0
N B:CYS196 4.0 92.8 1.0
CD2 B:HIS213 4.3 100.2 1.0
NE2 B:HIS213 4.3 99.9 1.0
N B:HIS213 4.3 114.3 1.0
CA B:CYS196 4.3 87.7 1.0
CA B:HIS213 4.4 116.5 1.0
CA B:CYS193 4.8 84.9 1.0
CB B:ALA195 4.9 100.1 1.0
CA B:HIS216 4.9 134.7 1.0

Zinc binding site 4 out of 4 in 7lt9

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Zinc binding site 4 out of 4 in the Crystal Structure of Ras Suppressor-1 in Complex with Pinch-1 LIM4-5 Domains


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 Ras Suppressor-1 in Complex with Pinch-1 LIM4-5 Domains within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:170.6
occ:1.00
ND1 B:HIS243 2.2 160.6 1.0
SG B:CYS219 2.2 188.7 1.0
SG B:CYS222 2.2 182.7 1.0
SG B:CYS240 2.3 162.8 1.0
CG B:HIS243 3.1 157.6 1.0
CE1 B:HIS243 3.2 155.1 1.0
CB B:HIS243 3.4 152.8 1.0
CB B:CYS219 3.5 175.3 1.0
CB B:CYS222 3.8 166.8 1.0
CB B:CYS240 3.9 163.6 1.0
N B:CYS222 4.2 154.5 1.0
CD2 B:HIS243 4.2 151.0 1.0
NE2 B:HIS243 4.2 147.7 1.0
N B:CYS240 4.3 163.5 1.0
CA B:CYS222 4.6 161.4 1.0
CA B:HIS243 4.6 147.9 1.0
O B:CYS222 4.6 164.0 1.0
N B:HIS243 4.7 147.5 1.0
CA B:CYS240 4.7 164.1 1.0
CA B:CYS219 4.9 157.9 1.0

Reference:

K.Fukuda, F.Lu, J.Qin. Molecular Basis For Ras Suppressor-1 Binding to Pinch-1 in Focal Adhesion Assembly J.Biol.Chem. 2021.
ISSN: ESSN 1083-351X
Page generated: Mon Jul 12 17:23:39 2021

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