Atomistry » Zinc » PDB 3dsv-3e2c » 3dug
Atomistry »
  Zinc »
    PDB 3dsv-3e2c »
      3dug »

Zinc in PDB 3dug: Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc

Protein crystallography data

The structure of Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc, PDB code: 3dug was solved by Y.Patskovsky, U.A.Ramagopal, R.Toro, A.J.Meyer, J.Freeman, M.Iizuka, K.Bain, L.Rodgers, F.Raushel, J.M.Sauder, S.K.Burley, S.C.Almo, New Yorksgx Research Center For Structural Genomics (Nysgxrc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.62
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 113.325, 146.040, 255.646, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 26.4

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc (pdb code 3dug). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 32 binding sites of Zinc where determined in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc, PDB code: 3dug:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 32 in 3dug

Go back to Zinc Binding Sites List in 3dug
Zinc binding site 1 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


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 Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn425

b:92.8
occ:1.00
NE2 A:HIS62 2.1 69.0 1.0
NE2 A:HIS64 2.4 81.1 1.0
OD1 A:ASP315 2.7 85.0 1.0
OD2 A:ASP315 2.7 85.3 1.0
CG A:ASP315 2.9 83.8 1.0
CD2 A:HIS62 3.0 68.7 1.0
CD2 A:HIS64 3.2 78.4 1.0
OQ2 A:KCX182 3.2 0.3 1.0
CE1 A:HIS62 3.2 69.9 1.0
CE1 A:HIS64 3.5 79.8 1.0
N A:ARG429 3.7 83.3 1.0
CX A:KCX182 3.7 0.1 1.0
OQ1 A:KCX182 3.8 98.1 1.0
ZN A:ZN428 3.8 0.3 0.8
CG A:HIS62 4.2 68.1 1.0
CG1 A:VAL105 4.2 67.8 1.0
ND1 A:HIS62 4.2 68.0 1.0
CB A:ASP315 4.3 82.7 1.0
CG A:HIS64 4.4 76.5 1.0
NE2 A:HIS243 4.4 78.7 1.0
CE1 A:HIS243 4.5 78.2 1.0
ND1 A:HIS64 4.5 79.0 1.0
NZ A:KCX182 4.6 95.5 1.0
CA A:ARG429 4.7 84.2 1.0
CA A:ASP315 4.7 82.2 1.0

Zinc binding site 2 out of 32 in 3dug

Go back to Zinc Binding Sites List in 3dug
Zinc binding site 2 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


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 Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn426

b:0.5
occ:1.00
NE2 A:HIS304 2.3 95.2 1.0
OE2 A:GLU340 2.4 76.2 1.0
OE1 A:GLU340 2.5 74.0 1.0
CD A:GLU340 2.8 77.1 1.0
CE1 A:HIS304 3.2 92.0 1.0
CD2 A:HIS304 3.3 92.5 1.0
O A:GLY335 3.9 84.0 1.0
ND1 A:HIS304 4.3 94.8 1.0
CG A:GLU340 4.3 72.7 1.0
CG A:HIS304 4.3 92.2 1.0
CG2 A:THR337 4.6 77.3 1.0
N A:THR337 4.7 79.0 1.0
CA A:MET336 4.8 79.4 1.0
C A:GLY335 5.0 82.7 1.0

Zinc binding site 3 out of 32 in 3dug

Go back to Zinc Binding Sites List in 3dug
Zinc binding site 3 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


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 Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn427

b:0.9
occ:1.00
OG1 A:THR128 2.4 68.5 1.0
OE2 A:GLU392 2.6 76.9 1.0
CB A:THR128 3.3 58.9 1.0
CD A:GLU392 3.5 75.1 1.0
CG A:GLU392 3.8 72.4 1.0
OD2 A:ASP368 3.9 68.4 1.0
CG2 A:THR128 4.0 51.4 1.0
OG1 A:THR101 4.2 67.0 1.0
OD1 A:ASP368 4.4 75.4 1.0
O A:THR100 4.4 63.7 1.0
CG A:ASP368 4.6 71.1 1.0
CA A:THR128 4.6 58.3 1.0
CE A:LYS391 4.6 63.7 1.0
OE1 A:GLU392 4.7 80.3 1.0
OD1 A:ASP366 4.7 75.2 1.0
N A:THR128 4.7 56.8 1.0
CG A:LYS391 4.8 73.2 1.0
CD A:LYS391 4.8 68.6 1.0

Zinc binding site 4 out of 32 in 3dug

Go back to Zinc Binding Sites List in 3dug
Zinc binding site 4 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


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 Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn428

b:0.3
occ:0.80
OQ1 A:KCX182 2.4 98.1 1.0
ND1 A:HIS223 2.4 86.0 1.0
NE2 A:HIS243 2.4 78.7 1.0
OQ2 A:KCX182 2.5 0.3 1.0
CX A:KCX182 2.7 0.1 1.0
CE1 A:HIS223 3.0 85.5 1.0
N A:ARG429 3.2 83.3 1.0
CA A:ARG429 3.2 84.2 1.0
CD2 A:HIS243 3.3 73.4 1.0
CE1 A:HIS243 3.3 78.2 1.0
CG A:HIS223 3.4 81.8 1.0
C A:ARG429 3.8 85.5 1.0
ZN A:ZN425 3.8 92.8 1.0
NE2 A:HIS142 3.8 84.2 1.0
CB A:HIS223 3.9 71.0 1.0
O A:ARG429 4.0 85.2 1.0
NZ A:KCX182 4.0 95.5 1.0
NE2 A:HIS223 4.2 87.4 1.0
CD2 A:HIS142 4.3 79.7 1.0
CE1 A:HIS62 4.3 69.9 1.0
NE2 A:HIS62 4.3 69.0 1.0
OD2 A:ASP315 4.4 85.3 1.0
ND1 A:HIS243 4.4 77.6 1.0
CD2 A:HIS223 4.4 83.9 1.0
CG A:HIS243 4.4 73.7 1.0
CB A:ARG429 4.6 85.0 1.0
OXT A:ARG429 4.6 86.5 1.0
CA A:HIS223 4.9 67.9 1.0
CE A:KCX182 4.9 87.3 1.0
CE1 A:HIS142 4.9 83.1 1.0

Zinc binding site 5 out of 32 in 3dug

Go back to Zinc Binding Sites List in 3dug
Zinc binding site 5 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn425

b:85.3
occ:1.00
NE2 B:HIS62 2.1 70.3 1.0
NE2 B:HIS64 2.6 79.2 1.0
OD2 B:ASP315 2.6 88.3 1.0
OD1 B:ASP315 2.8 87.6 1.0
OQ2 B:KCX182 3.0 0.7 1.0
CG B:ASP315 3.0 86.2 1.0
CD2 B:HIS62 3.1 66.3 1.0
CE1 B:HIS62 3.1 69.8 1.0
N B:ARG429 3.4 67.4 1.0
CD2 B:HIS64 3.4 77.3 1.0
CX B:KCX182 3.5 0.1 1.0
OQ1 B:KCX182 3.6 99.5 1.0
CE1 B:HIS64 3.6 79.1 1.0
ZN B:ZN428 3.7 87.2 0.8
NE2 B:HIS243 4.1 82.2 1.0
ND1 B:HIS62 4.2 68.0 1.0
CG B:HIS62 4.2 64.9 1.0
CB B:ASP315 4.3 82.2 1.0
CG1 B:VAL105 4.3 70.6 1.0
CE1 B:HIS243 4.3 75.2 1.0
CA B:ARG429 4.5 73.4 1.0
NZ B:KCX182 4.6 94.9 1.0
CG B:HIS64 4.6 74.1 1.0
ND1 B:HIS64 4.7 76.8 1.0
CA B:ASP315 4.8 80.8 1.0

Zinc binding site 6 out of 32 in 3dug

Go back to Zinc Binding Sites List in 3dug
Zinc binding site 6 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn426

b:77.5
occ:0.50
OE2 B:GLU340 2.4 69.3 1.0
NE2 B:HIS304 2.5 95.4 1.0
OE1 B:GLU340 2.7 68.1 1.0
CD B:GLU340 3.0 71.5 1.0
CE1 B:HIS304 3.4 94.0 1.0
CD2 B:HIS304 3.4 92.0 1.0
O B:GLY335 4.1 80.5 1.0
ND1 B:HIS304 4.4 92.6 1.0
CG B:GLU340 4.5 69.3 1.0
CG B:HIS304 4.5 90.5 1.0
CG2 B:THR337 4.7 75.5 1.0

Zinc binding site 7 out of 32 in 3dug

Go back to Zinc Binding Sites List in 3dug
Zinc binding site 7 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn427

b:80.9
occ:0.50
OG1 B:THR128 2.3 63.3 1.0
OE2 B:GLU392 2.5 73.0 1.0
CB B:THR128 3.2 57.2 1.0
CD B:GLU392 3.5 74.0 1.0
CG2 B:THR128 3.8 50.8 1.0
CG B:GLU392 3.8 74.1 1.0
OD2 B:ASP368 4.1 73.4 1.0
OG1 B:THR101 4.3 65.5 1.0
CA B:THR128 4.5 54.7 1.0
OE1 B:GLU392 4.6 79.0 1.0
OD1 B:ASP366 4.6 79.2 1.0
O B:THR100 4.6 67.0 1.0
OD1 B:ASP368 4.7 73.1 1.0
N B:THR128 4.8 54.3 1.0
CG B:ASP368 4.8 73.4 1.0
CE B:LYS391 4.8 67.2 1.0
CD B:LYS391 5.0 71.1 1.0

Zinc binding site 8 out of 32 in 3dug

Go back to Zinc Binding Sites List in 3dug
Zinc binding site 8 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn428

b:87.2
occ:0.80
ND1 B:HIS223 2.2 79.1 1.0
OQ1 B:KCX182 2.3 99.5 1.0
NE2 B:HIS243 2.4 82.2 1.0
OQ2 B:KCX182 2.6 0.7 1.0
CX B:KCX182 2.7 0.1 1.0
CE1 B:HIS223 3.0 83.1 1.0
CD2 B:HIS243 3.1 79.4 1.0
CG B:HIS223 3.2 77.1 1.0
N B:ARG429 3.3 67.4 1.0
CA B:ARG429 3.4 73.4 1.0
CE1 B:HIS243 3.5 75.2 1.0
CB B:HIS223 3.6 66.7 1.0
ZN B:ZN425 3.7 85.3 1.0
NE2 B:HIS142 3.9 84.8 1.0
NZ B:KCX182 4.0 94.9 1.0
C B:ARG429 4.1 69.6 1.0
NE2 B:HIS223 4.1 85.1 1.0
O B:ARG429 4.1 61.2 1.0
CD2 B:HIS223 4.2 81.8 1.0
CE1 B:HIS62 4.3 69.8 1.0
CD2 B:HIS142 4.3 79.5 1.0
CG B:HIS243 4.3 72.8 1.0
NE2 B:HIS62 4.4 70.3 1.0
ND1 B:HIS243 4.4 72.4 1.0
OD2 B:ASP315 4.5 88.3 1.0
CA B:HIS223 4.6 65.2 1.0
CE B:KCX182 4.7 83.4 1.0
CB B:ARG429 4.8 74.7 1.0
CE1 B:HIS142 5.0 83.6 1.0
OXT B:ARG429 5.0 66.7 1.0

Zinc binding site 9 out of 32 in 3dug

Go back to Zinc Binding Sites List in 3dug
Zinc binding site 9 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn425

b:93.2
occ:1.00
NE2 C:HIS62 2.1 70.1 1.0
NE2 C:HIS64 2.5 80.6 1.0
OD2 C:ASP315 2.8 87.3 1.0
OD1 C:ASP315 2.8 90.0 1.0
CD2 C:HIS62 3.0 69.4 1.0
CG C:ASP315 3.1 86.5 1.0
CE1 C:HIS62 3.1 73.0 1.0
OQ2 C:KCX182 3.1 0.7 1.0
CD2 C:HIS64 3.3 77.5 1.0
N C:ARG429 3.4 85.0 1.0
CE1 C:HIS64 3.5 78.8 1.0
CX C:KCX182 3.6 0.6 1.0
ZN C:ZN428 3.7 0.2 0.8
OQ1 C:KCX182 3.7 97.7 1.0
ND1 C:HIS62 4.2 73.4 1.0
CG C:HIS62 4.2 68.3 1.0
CG1 C:VAL105 4.3 67.7 1.0
NE2 C:HIS243 4.3 84.4 1.0
CE1 C:HIS243 4.4 82.1 1.0
CB C:ASP315 4.4 81.6 1.0
CG C:HIS64 4.5 73.4 1.0
NZ C:KCX182 4.6 95.8 1.0
ND1 C:HIS64 4.6 78.5 1.0
CA C:ASP315 4.8 81.0 1.0
CA C:ARG429 4.8 89.7 1.0

Zinc binding site 10 out of 32 in 3dug

Go back to Zinc Binding Sites List in 3dug
Zinc binding site 10 out of 32 in the Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Zn-Dependent Arginine Carboxypeptidase Complexed with Zinc within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn426

b:0.9
occ:1.00
NE2 C:HIS304 2.5 96.8 1.0
OE1 C:GLU340 2.6 75.2 1.0
OE2 C:GLU340 2.6 69.6 1.0
O C:HOH455 2.6 69.7 1.0
CD C:GLU340 2.9 75.0 1.0
CD2 C:HIS304 3.4 95.5 1.0
CE1 C:HIS304 3.5 92.8 1.0
O C:GLY335 3.9 86.4 1.0
CG C:GLU340 4.5 72.7 1.0
ND1 C:HIS304 4.5 92.5 1.0
CG2 C:THR337 4.5 77.0 1.0
CG C:HIS304 4.6 91.9 1.0
N C:THR337 4.8 78.8 1.0
CA C:MET336 4.8 78.9 1.0

Reference:

D.F.Xiang, Y.Patskovsky, C.Xu, A.J.Meyer, J.M.Sauder, S.K.Burley, S.C.Almo, F.M.Raushel. Functional Identification of Incorrectly Annotated Prolidases From the Amidohydrolase Superfamily of Enzymes. Biochemistry V. 48 3730 2009.
ISSN: ISSN 0006-2960
PubMed: 19281183
DOI: 10.1021/BI900111Q
Page generated: Thu Oct 24 12:20:37 2024

Last articles

Zn in 9FD2
Zn in 9GUW
Zn in 9GUX
Zn in 9F7C
Zn in 9GUR
Zn in 9F7A
Zn in 9DDE
Zn in 9DBY
Zn in 9EBZ
Zn in 9DGG
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy