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Zinc in PDB 3naa: Crystal Structure of FAB15 MUT5

Protein crystallography data

The structure of Crystal Structure of FAB15 MUT5, PDB code: 3naa 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) 30.56 / 1.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.534, 74.784, 65.198, 90.00, 103.50, 90.00
R / Rfree (%) 17.8 / 20

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of FAB15 MUT5 (pdb code 3naa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of FAB15 MUT5, PDB code: 3naa:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in 3naa

Go back to Zinc Binding Sites List in 3naa
Zinc binding site 1 out of 3 in the Crystal Structure of FAB15 MUT5


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 MUT5 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn215

b:25.5
occ:1.00
OD2 L:ASP151 1.9 22.2 1.0
OXT L:ACT216 2.0 27.8 1.0
ND1 L:HIS189 2.1 23.2 1.0
C L:ACT216 2.8 26.6 1.0
O L:ACT216 2.8 36.1 1.0
CG L:ASP151 2.9 21.4 1.0
CE1 L:HIS189 2.9 29.7 1.0
CG L:HIS189 3.2 24.1 1.0
CB L:ASP151 3.4 20.9 1.0
CB L:HIS189 3.6 23.4 1.0
CA L:HIS189 3.8 20.6 1.0
OD1 L:ASP151 4.0 22.1 1.0
NE2 L:HIS189 4.1 30.0 1.0
O L:LYS188 4.2 26.8 1.0
CH3 L:ACT216 4.2 33.9 1.0
CD2 L:HIS189 4.3 24.8 1.0
N L:HIS189 4.5 24.0 1.0
C L:LYS188 4.6 27.7 1.0
CA L:ASP151 4.8 21.1 1.0
C L:HIS189 5.0 22.0 1.0
N L:LYS190 5.0 23.0 1.0

Zinc binding site 2 out of 3 in 3naa

Go back to Zinc Binding Sites List in 3naa
Zinc binding site 2 out of 3 in the Crystal Structure of FAB15 MUT5


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 MUT5 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn218

b:33.9
occ:1.00
O L:CYS214 1.9 33.5 1.0
NE2 H:HIS213 2.1 28.9 1.0
NE2 H:HIS217 2.2 39.6 1.0
O H:ACT220 2.3 42.2 1.0
OXT H:ACT220 2.4 39.9 1.0
C L:CYS214 2.7 34.9 1.0
C H:ACT220 2.7 46.0 1.0
OXT L:CYS214 2.7 32.9 1.0
CD2 H:HIS213 3.0 35.6 1.0
CE1 H:HIS217 3.1 41.3 1.0
CE1 H:HIS213 3.1 30.1 1.0
CD2 H:HIS217 3.3 44.6 1.0
O H:HIS214 3.3 43.8 1.0
CA L:CYS214 4.2 39.2 1.0
CH3 H:ACT220 4.2 44.9 1.0
CG H:HIS213 4.2 31.2 1.0
ND1 H:HIS213 4.2 28.8 1.0
OG H:SER128 4.2 49.3 1.0
ND1 H:HIS217 4.2 44.2 1.0
O L:HOH281 4.3 50.5 1.0
CG H:HIS217 4.4 48.5 1.0
C H:HIS214 4.5 36.8 1.0
N L:CYS214 4.7 33.8 1.0
CB L:CYS214 4.7 46.5 1.0
SG L:CYS214 4.8 48.6 1.0
CA H:HIS215 4.8 45.1 1.0
C H:HIS215 4.9 48.1 1.0
N H:SER128 4.9 36.1 1.0

Zinc binding site 3 out of 3 in 3naa

Go back to Zinc Binding Sites List in 3naa
Zinc binding site 3 out of 3 in the Crystal Structure of FAB15 MUT5


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 MUT5 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn219

b:47.9
occ:1.00
OD2 H:ASP54 2.2 55.0 1.0
OD2 H:ASP52 2.3 60.2 1.0
OD1 H:ASP54 2.8 57.8 1.0
CG H:ASP54 2.8 60.7 1.0
CG H:ASP52 3.2 52.3 1.0
CB H:ASP52 3.6 48.2 1.0
OD1 H:ASP52 4.2 47.7 1.0
CB H:ASP54 4.3 63.4 1.0
CB H:TYR56 4.4 47.0 1.0
OG H:SER53 4.4 57.2 1.0
CZ2 H:TRP33 4.6 54.3 1.0
NE1 H:TRP33 4.7 40.5 1.0
CE2 H:TRP33 4.9 45.4 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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