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Zinc in PDB 3ncj: Crystal Structure of FAB15 MUT8

Protein crystallography data

The structure of Crystal Structure of FAB15 MUT8, PDB code: 3ncj was solved by J.Luo, Y.Feng, G.L.Gilliland, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.18 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.550, 74.700, 65.390, 90.00, 104.23, 90.00
R / Rfree (%) 20 / 22.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of FAB15 MUT8 (pdb code 3ncj). 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 FAB15 MUT8, PDB code: 3ncj:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3ncj

Go back to Zinc Binding Sites List in 3ncj
Zinc binding site 1 out of 4 in the Crystal Structure of FAB15 MUT8


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 FAB15 MUT8 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn215

b:14.9
occ:0.82
OD2 L:ASP151 1.9 14.3 1.0
OXT L:ACT217 1.9 17.6 1.0
ND1 L:HIS189 2.1 15.4 1.0
C L:ACT217 2.8 15.6 1.0
O L:ACT217 2.8 24.1 1.0
CG L:ASP151 2.9 16.7 1.0
CE1 L:HIS189 3.0 19.6 1.0
CG L:HIS189 3.2 13.9 1.0
CB L:ASP151 3.5 13.2 1.0
CB L:HIS189 3.6 13.8 1.0
CA L:HIS189 3.8 12.0 1.0
OD1 L:ASP151 4.0 14.8 1.0
NE2 L:HIS189 4.1 20.5 1.0
O L:LYS188 4.2 17.9 1.0
CH3 L:ACT217 4.2 27.2 1.0
CD2 L:HIS189 4.3 14.1 1.0
N L:HIS189 4.4 13.9 1.0
C L:LYS188 4.6 19.4 1.0
CA L:ASP151 4.9 13.6 1.0
C L:HIS189 4.9 14.8 1.0
N L:LYS190 5.0 13.5 1.0

Zinc binding site 2 out of 4 in 3ncj

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Zinc binding site 2 out of 4 in the Crystal Structure of FAB15 MUT8


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 FAB15 MUT8 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn216

b:20.3
occ:0.40
O L:HOH330 2.2 20.0 1.0
OD1 L:ASN137 2.2 33.5 1.0
OD1 L:ASN138 2.2 24.6 1.0
O H:HOH245 2.3 26.2 1.0
NE2 H:HIS164 2.3 25.5 1.0
O L:HOH380 2.6 48.8 1.0
CD2 H:HIS164 2.8 20.9 1.0
CG L:ASN137 2.9 24.2 1.0
ND2 L:ASN137 3.1 28.6 1.0
CG L:ASN138 3.2 29.7 1.0
CE1 H:HIS164 3.5 24.8 1.0
ND2 L:ASN138 3.7 38.8 1.0
CG H:HIS164 4.1 18.1 1.0
OG L:SER174 4.1 13.0 1.0
O L:HOH400 4.3 39.4 1.0
CB L:ASN137 4.3 16.5 1.0
CB L:ASN138 4.3 22.2 1.0
OG1 H:THR183 4.4 31.7 1.0
O H:GLY162 4.4 20.9 1.0
ND1 H:HIS164 4.4 21.2 1.0
O H:HOH258 4.4 48.7 1.0
N L:ASN138 4.5 14.1 1.0
CA L:ASN137 4.8 13.0 1.0
CG2 H:THR183 4.8 33.2 1.0
O L:HOH246 4.9 16.0 1.0
C L:ASN137 4.9 15.8 1.0
CA L:ASN138 4.9 17.0 1.0

Zinc binding site 3 out of 4 in 3ncj

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Zinc binding site 3 out of 4 in the Crystal Structure of FAB15 MUT8


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 FAB15 MUT8 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn218

b:18.5
occ:0.77
O L:CYS214 1.9 19.8 1.0
O H:ACT220 2.0 25.8 1.0
NE2 H:HIS213 2.0 18.5 1.0
NE2 H:HIS217 2.1 25.5 1.0
OXT H:ACT220 2.6 25.7 1.0
C H:ACT220 2.7 27.2 1.0
C L:CYS214 2.7 20.7 1.0
OXT L:CYS214 2.9 18.8 1.0
CD2 H:HIS213 3.0 19.2 1.0
CE1 H:HIS213 3.0 18.7 1.0
CE1 H:HIS217 3.1 25.0 1.0
CD2 H:HIS217 3.2 23.9 1.0
O H:HIS214 3.4 24.5 1.0
ND1 H:HIS213 4.1 20.3 1.0
CG H:HIS213 4.1 19.4 1.0
CH3 H:ACT220 4.2 30.2 1.0
CA L:CYS214 4.2 21.4 1.0
ND1 H:HIS217 4.2 27.7 1.0
OG H:SER128 4.2 28.3 1.0
O L:HOH447 4.2 29.0 1.0
CG H:HIS217 4.3 27.7 1.0
C H:HIS214 4.6 24.1 1.0
CB L:CYS214 4.7 22.5 1.0
SG L:CYS214 4.7 23.6 1.0
N L:CYS214 4.8 20.0 1.0
C H:HIS215 4.8 31.6 1.0
CA H:HIS215 4.8 30.7 1.0
N H:SER128 4.9 20.5 1.0
CB H:SER128 4.9 26.0 1.0
O H:HIS215 5.0 31.6 1.0

Zinc binding site 4 out of 4 in 3ncj

Go back to Zinc Binding Sites List in 3ncj
Zinc binding site 4 out of 4 in the Crystal Structure of FAB15 MUT8


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 FAB15 MUT8 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn219

b:27.4
occ:0.78
OD2 H:ASP54 2.1 32.4 1.0
OD2 H:ASP52 2.2 35.3 1.0
CG H:ASP54 2.8 33.9 1.0
OD1 H:ASP54 2.8 34.4 1.0
CG H:ASP52 3.1 29.2 1.0
CB H:ASP52 3.6 24.0 1.0
O H:HOH311 4.1 41.0 1.0
OD1 H:ASP52 4.2 27.2 1.0
CB H:TYR56 4.2 28.6 1.0
CB H:ASP54 4.2 36.0 1.0
OG H:SER53 4.3 33.6 1.0
CZ2 H:TRP33 4.6 33.9 1.0
NE1 H:TRP33 4.8 25.9 1.0
CG H:TYR56 4.9 27.5 1.0
CE2 H:TRP33 4.9 28.6 1.0

Reference:

J.Luo, Y.Feng, G.L.Gilliland. Co-Evolution of Antibody Stability and Vk Cdr-L3 Canonical Structure To Be Published.
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