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Zinc in PDB 3edg: Crystal Structure of Bone Morphogenetic Protein 1 Protease Domain

Enzymatic activity of Crystal Structure of Bone Morphogenetic Protein 1 Protease Domain

All present enzymatic activity of Crystal Structure of Bone Morphogenetic Protein 1 Protease Domain:
3.4.24.19;

Protein crystallography data

The structure of Crystal Structure of Bone Morphogenetic Protein 1 Protease Domain, PDB code: 3edg was solved by A.Mac Sweeney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.02 / 1.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.432, 57.260, 68.800, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 17.7

Zinc Binding Sites:

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

Zinc binding site 1 out of 2 in 3edg

Go back to Zinc Binding Sites List in 3edg
Zinc binding site 1 out of 2 in the Crystal Structure of Bone Morphogenetic Protein 1 Protease Domain


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 Bone Morphogenetic Protein 1 Protease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn210

b:6.9
occ:1.00
NE2 A:HIS92 2.1 6.7 1.0
NE2 A:HIS102 2.1 5.8 1.0
NE2 A:HIS96 2.1 5.7 1.0
CE1 A:HIS102 3.0 7.0 1.0
CD2 A:HIS102 3.0 6.8 1.0
CD2 A:HIS92 3.1 7.2 1.0
CE1 A:HIS92 3.1 6.4 1.0
CE1 A:HIS96 3.1 6.3 1.0
CD2 A:HIS96 3.1 5.9 1.0
O A:HOH480 4.1 26.9 1.0
OE2 A:GLU93 4.1 16.7 1.0
ND1 A:HIS102 4.1 7.1 1.0
CG A:HIS102 4.2 6.2 1.0
ND1 A:HIS92 4.2 6.8 1.0
ND1 A:HIS96 4.2 6.2 1.0
CG A:HIS92 4.2 5.7 1.0
O A:HOH331 4.2 20.4 1.0
CG A:HIS96 4.3 6.3 1.0
O A:HOH510 4.6 37.0 1.0
O A:HOH342 4.6 19.7 1.0
CE A:MET147 4.7 7.4 1.0
O A:HOH418 4.8 24.6 1.0
CD A:GLU93 4.8 12.8 1.0
OE1 A:GLU93 4.9 15.7 1.0
O A:HOH384 4.9 21.6 1.0
O A:HOH555 4.9 39.1 1.0

Zinc binding site 2 out of 2 in 3edg

Go back to Zinc Binding Sites List in 3edg
Zinc binding site 2 out of 2 in the Crystal Structure of Bone Morphogenetic Protein 1 Protease Domain


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 Bone Morphogenetic Protein 1 Protease Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn211

b:5.0
occ:0.50
O A:ACE201 2.3 6.0 1.0
O A:HOH221 2.4 9.2 1.0
O A:HOH214 2.4 8.1 1.0
O A:HOH218 2.4 8.2 1.0
NE2 A:GLN189 2.4 5.1 1.0
OE1 A:GLU103 2.5 7.0 1.0
OE2 A:GLU103 2.5 6.5 1.0
CD A:GLU103 2.8 6.2 1.0
C A:ACE201 3.3 6.7 1.0
CD A:GLN189 3.5 8.1 1.0
OE1 A:GLN189 3.8 10.3 1.0
N A:ALA1 3.9 5.7 1.0
O A:HOH216 4.0 7.5 1.0
CB A:ASP142 4.2 7.0 1.0
NH1 A:ARG106 4.2 7.2 1.0
CG A:GLU103 4.4 6.5 1.0
CH3 A:ACE201 4.5 2.8 1.0
O A:HOH231 4.5 12.0 1.0
OG A:SER145 4.7 6.8 1.0
OD1 A:ASP186 4.7 9.8 1.0
CG A:GLN189 4.8 11.6 1.0
OD2 A:ASP142 4.8 7.7 1.0
N A:ASP142 4.8 6.3 1.0
CB A:SER145 4.8 6.4 1.0
O A:THR140 4.9 7.8 1.0
CB A:GLN189 4.9 11.0 1.0
CD A:ARG106 4.9 5.8 1.0
CE2 A:PHE100 5.0 11.0 1.0

Reference:

A.Mac Sweeney, S.G.Parrado, D.Vinzenz, A.Bernardi, A.Hein, U.Bodendorf, P.Erbel, C.Logel, B.Gerhartz. Structural Basis For the Substrate Specificity of Bone Morphogenetic Protein 1/Tolloid-Like Metalloproteases To Be Published.
Page generated: Wed Dec 16 04:15:38 2020

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