Atomistry » Zinc » PDB 3mho-3mpg » 3mkv
Atomistry »
  Zinc »
    PDB 3mho-3mpg »
      3mkv »

Zinc in PDB 3mkv: Crystal Structure of Amidohydrolase EAJ56179

Protein crystallography data

The structure of Crystal Structure of Amidohydrolase EAJ56179, PDB code: 3mkv was solved by Y.Patskovsky, J.Bonanno, S.Ozyurt, J.M.Sauder, J.Freeman, B.Wu, D.Smith, K.Bain, L.Rodgers, S.R.Wasserman, F.M.Raushel, S.K.Burley, S.C.Almo, Newyork Sgx 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) 40.00 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 92.022, 198.599, 104.294, 90.00, 107.76, 90.00
R / Rfree (%) 17.1 / 22.9

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of Amidohydrolase EAJ56179 (pdb code 3mkv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 16 binding sites of Zinc where determined in the Crystal Structure of Amidohydrolase EAJ56179, PDB code: 3mkv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 16 in 3mkv

Go back to Zinc Binding Sites List in 3mkv
Zinc binding site 1 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn425

b:59.7
occ:1.00
NE2 A:HIS63 2.1 37.3 1.0
NE2 A:HIS65 2.1 54.4 1.0
OQ2 A:KCX191 2.3 66.2 1.0
OD1 A:ASP324 2.4 64.4 1.0
CD2 A:HIS63 3.0 44.4 1.0
CD2 A:HIS65 3.0 53.2 1.0
CG A:ASP324 3.0 53.1 1.0
CE1 A:HIS63 3.1 43.9 1.0
CE1 A:HIS65 3.1 45.4 1.0
CX A:KCX191 3.2 57.7 1.0
OD2 A:ASP324 3.3 55.9 1.0
ZN A:ZN426 3.3 66.3 1.0
OQ1 A:KCX191 3.5 61.7 1.0
O A:HOH559 3.8 87.0 1.0
O A:HOH435 4.1 63.9 1.0
CG A:HIS63 4.1 42.4 1.0
CB A:ASP324 4.2 46.4 1.0
ND1 A:HIS63 4.2 49.4 1.0
CG A:HIS65 4.2 44.8 1.0
ND1 A:HIS65 4.2 43.9 1.0
CB A:ALA106 4.3 52.0 1.0
NZ A:KCX191 4.3 51.4 1.0
NE2 A:HIS252 4.4 52.4 1.0
CE1 A:HIS252 4.6 54.9 1.0
CA A:ASP324 4.8 46.5 1.0
O4 A:SO4427 4.9 57.6 0.5

Zinc binding site 2 out of 16 in 3mkv

Go back to Zinc Binding Sites List in 3mkv
Zinc binding site 2 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn426

b:66.3
occ:1.00
OQ1 A:KCX191 2.2 61.7 1.0
ND1 A:HIS232 2.4 57.5 1.0
NE2 A:HIS252 2.4 52.4 1.0
CX A:KCX191 3.0 57.7 1.0
OQ2 A:KCX191 3.1 66.2 1.0
O4 A:SO4427 3.2 57.6 0.5
CD2 A:HIS252 3.3 51.7 1.0
ZN A:ZN425 3.3 59.7 1.0
CE1 A:HIS232 3.3 48.4 1.0
CG A:HIS232 3.4 50.0 1.0
O A:HOH435 3.5 63.9 1.0
CE1 A:HIS252 3.5 54.9 1.0
CB A:HIS232 3.7 49.8 1.0
CE1 A:HIS63 3.9 43.9 1.0
NE2 A:HIS63 3.9 37.3 1.0
OD2 A:ASP324 4.0 55.9 1.0
NZ A:KCX191 4.3 51.4 1.0
NE2 A:HIS140 4.4 66.7 1.0
NE2 A:HIS232 4.5 57.3 1.0
CG A:HIS252 4.5 55.0 1.0
CD2 A:HIS232 4.5 51.9 1.0
ND1 A:HIS252 4.6 65.0 1.0
CD2 A:HIS140 4.6 63.7 1.0
S A:SO4427 4.6 64.1 0.5
CG A:ASP324 4.7 53.1 1.0
O A:HOH559 4.8 87.0 1.0
CA A:HIS232 4.8 54.6 1.0
OD1 A:ASP324 4.8 64.4 1.0
CE A:KCX191 4.8 41.6 1.0
SD A:MET193 4.9 43.1 1.0
O2 A:SO4427 5.0 64.1 0.5

Zinc binding site 3 out of 16 in 3mkv

Go back to Zinc Binding Sites List in 3mkv
Zinc binding site 3 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn425

b:62.8
occ:1.00
OQ2 B:KCX191 2.1 63.9 1.0
NE2 B:HIS65 2.1 46.6 1.0
NE2 B:HIS63 2.1 42.1 1.0
OD1 B:ASP324 2.2 54.6 1.0
O B:HOH546 2.4 58.1 1.0
CG B:ASP324 2.9 52.0 1.0
CE1 B:HIS65 3.0 42.3 1.0
CX B:KCX191 3.1 67.4 1.0
CD2 B:HIS63 3.1 43.4 1.0
CD2 B:HIS65 3.1 39.3 1.0
CE1 B:HIS63 3.1 51.0 1.0
OD2 B:ASP324 3.3 49.3 1.0
OQ1 B:KCX191 3.3 64.6 1.0
ZN B:ZN426 3.5 66.6 1.0
CB B:ASP324 4.1 48.8 1.0
ND1 B:HIS65 4.2 50.3 1.0
CB B:ALA106 4.2 40.6 1.0
O B:HOH513 4.2 68.2 1.0
NZ B:KCX191 4.2 55.8 1.0
ND1 B:HIS63 4.2 46.7 1.0
CG B:HIS65 4.2 49.7 1.0
CG B:HIS63 4.2 44.1 1.0
NE2 B:HIS252 4.4 53.4 1.0
CE1 B:HIS252 4.4 50.3 1.0
O3 B:SO4427 4.8 64.5 0.5
CA B:ASP324 4.9 45.3 1.0

Zinc binding site 4 out of 16 in 3mkv

Go back to Zinc Binding Sites List in 3mkv
Zinc binding site 4 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn426

b:66.6
occ:1.00
O B:HOH546 2.1 58.1 1.0
OQ1 B:KCX191 2.2 64.6 1.0
NE2 B:HIS252 2.2 53.4 1.0
ND1 B:HIS232 2.3 50.1 1.0
CX B:KCX191 3.0 67.4 1.0
CD2 B:HIS252 3.1 44.6 1.0
O3 B:SO4427 3.2 64.5 0.5
CE1 B:HIS232 3.2 51.5 1.0
CE1 B:HIS252 3.2 50.3 1.0
OQ2 B:KCX191 3.3 63.9 1.0
CG B:HIS232 3.3 55.0 1.0
ZN B:ZN425 3.5 62.8 1.0
CB B:HIS232 3.6 45.7 1.0
CE1 B:HIS63 4.0 51.0 1.0
NE2 B:HIS63 4.1 42.1 1.0
NZ B:KCX191 4.2 55.8 1.0
O B:HOH513 4.2 68.2 1.0
CG B:HIS252 4.3 56.4 1.0
ND1 B:HIS252 4.3 53.1 1.0
NE2 B:HIS232 4.3 57.4 1.0
CD2 B:HIS232 4.4 49.9 1.0
OD2 B:ASP324 4.4 49.3 1.0
S B:SO4427 4.4 77.2 0.5
CA B:HIS232 4.5 46.0 1.0
NE2 B:HIS140 4.6 72.0 1.0
CE B:KCX191 4.7 42.0 1.0
CD2 B:HIS140 4.7 72.1 1.0
SD B:MET193 4.8 44.0 1.0
O4 B:SO4427 4.8 66.7 0.5
O1 B:SO4427 4.9 73.6 0.5
CB B:GLU251 4.9 41.2 1.0
CG B:ASP324 5.0 52.0 1.0

Zinc binding site 5 out of 16 in 3mkv

Go back to Zinc Binding Sites List in 3mkv
Zinc binding site 5 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn425

b:63.5
occ:1.00
NE2 C:HIS63 2.0 50.6 1.0
NE2 C:HIS65 2.2 55.7 1.0
OD1 C:ASP324 2.3 59.2 1.0
OQ2 C:KCX191 2.4 65.4 1.0
CE1 C:HIS63 2.9 47.8 1.0
CD2 C:HIS63 3.0 40.5 1.0
CG C:ASP324 3.1 55.1 1.0
CX C:KCX191 3.1 60.0 1.0
CE1 C:HIS65 3.2 57.0 1.0
CD2 C:HIS65 3.2 59.2 1.0
O C:HOH557 3.3 70.1 1.0
ZN C:ZN426 3.3 66.2 1.0
OQ1 C:KCX191 3.3 61.3 1.0
OD2 C:ASP324 3.5 58.7 1.0
O C:HOH535 3.9 90.0 1.0
ND1 C:HIS63 4.1 49.9 1.0
CG C:HIS63 4.1 52.6 1.0
NE2 C:HIS252 4.2 43.2 1.0
NZ C:KCX191 4.2 50.4 1.0
CE1 C:HIS252 4.3 41.6 1.0
ND1 C:HIS65 4.3 60.2 1.0
CB C:ASP324 4.3 52.3 1.0
CB C:ALA106 4.3 50.3 1.0
CG C:HIS65 4.4 60.6 1.0
O4 C:SO4427 4.9 49.6 0.5

Zinc binding site 6 out of 16 in 3mkv

Go back to Zinc Binding Sites List in 3mkv
Zinc binding site 6 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn426

b:66.2
occ:1.00
OQ1 C:KCX191 2.2 61.3 1.0
NE2 C:HIS252 2.2 43.2 1.0
O C:HOH557 2.3 70.1 1.0
ND1 C:HIS232 2.4 55.6 1.0
CD2 C:HIS252 3.1 45.6 1.0
CX C:KCX191 3.1 60.0 1.0
CE1 C:HIS252 3.2 41.6 1.0
CE1 C:HIS232 3.3 50.9 1.0
ZN C:ZN425 3.3 63.5 1.0
CG C:HIS232 3.3 55.0 1.0
OQ2 C:KCX191 3.3 65.4 1.0
O4 C:SO4427 3.6 49.6 0.5
CB C:HIS232 3.6 47.4 1.0
CE1 C:HIS63 3.9 47.8 1.0
NE2 C:HIS63 4.1 50.6 1.0
CG C:HIS252 4.2 43.0 1.0
ND1 C:HIS252 4.3 45.4 1.0
NZ C:KCX191 4.3 50.4 1.0
NE2 C:HIS140 4.4 74.7 1.0
NE2 C:HIS232 4.4 55.6 1.0
CD2 C:HIS232 4.5 47.9 1.0
OD2 C:ASP324 4.5 58.7 1.0
CA C:HIS232 4.6 46.5 1.0
S C:SO4427 4.6 59.9 0.5
CD2 C:HIS140 4.6 70.5 1.0
O C:HOH535 4.7 90.0 1.0
O3 C:SO4427 4.7 48.0 0.5
CE C:KCX191 4.7 46.1 1.0
O2 C:SO4427 4.8 52.6 0.5
SD C:MET193 4.8 47.3 1.0
CB C:GLU251 4.9 46.2 1.0
OD1 C:ASP324 5.0 59.2 1.0
CG C:ASP324 5.0 55.1 1.0

Zinc binding site 7 out of 16 in 3mkv

Go back to Zinc Binding Sites List in 3mkv
Zinc binding site 7 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn425

b:63.8
occ:1.00
NE2 D:HIS65 1.8 52.5 1.0
OQ2 D:KCX191 2.2 63.5 1.0
NE2 D:HIS63 2.2 45.6 1.0
OD1 D:ASP324 2.3 58.0 1.0
CE1 D:HIS65 2.7 53.9 1.0
CD2 D:HIS65 2.9 53.5 1.0
CG D:ASP324 3.1 66.6 1.0
CD2 D:HIS63 3.1 56.2 1.0
CX D:KCX191 3.2 63.0 1.0
CE1 D:HIS63 3.2 48.8 1.0
OD2 D:ASP324 3.3 71.8 1.0
O D:HOH483 3.4 69.3 1.0
ZN D:ZN426 3.4 73.2 1.0
OQ1 D:KCX191 3.5 60.7 1.0
ND1 D:HIS65 3.8 59.4 1.0
CG D:HIS65 3.9 55.9 1.0
NZ D:KCX191 4.3 57.3 1.0
ND1 D:HIS63 4.3 40.1 1.0
CG D:HIS63 4.3 51.7 1.0
CE1 D:HIS252 4.3 69.1 1.0
CB D:ASP324 4.3 57.6 1.0
O D:HOH522 4.3 82.0 1.0
CB D:ALA106 4.4 50.3 1.0
NE2 D:HIS252 4.4 61.1 1.0
CA D:ASP324 4.9 56.8 1.0

Zinc binding site 8 out of 16 in 3mkv

Go back to Zinc Binding Sites List in 3mkv
Zinc binding site 8 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn426

b:73.2
occ:1.00
OQ1 D:KCX191 2.1 60.7 1.0
NE2 D:HIS252 2.2 61.1 1.0
ND1 D:HIS232 2.3 57.9 1.0
CX D:KCX191 3.0 63.0 1.0
CE1 D:HIS252 3.1 69.1 1.0
OQ2 D:KCX191 3.1 63.5 1.0
O D:HOH483 3.2 69.3 1.0
CD2 D:HIS252 3.2 61.3 1.0
CE1 D:HIS232 3.3 58.2 1.0
CG D:HIS232 3.3 49.5 1.0
ZN D:ZN425 3.4 63.8 1.0
CB D:HIS232 3.6 50.3 1.0
NE2 D:HIS63 4.0 45.6 1.0
CE1 D:HIS63 4.1 48.8 1.0
OD2 D:ASP324 4.2 71.8 1.0
NZ D:KCX191 4.2 57.3 1.0
ND1 D:HIS252 4.2 73.2 1.0
NE2 D:HIS140 4.3 72.3 1.0
CG D:HIS252 4.3 66.4 1.0
NE2 D:HIS232 4.4 58.8 1.0
CD2 D:HIS232 4.4 56.8 1.0
CD2 D:HIS140 4.5 71.3 1.0
CA D:HIS232 4.6 53.2 1.0
CE D:KCX191 4.8 50.8 1.0
SD D:MET193 4.8 55.7 1.0
O D:HOH529 4.8 61.0 1.0
CG D:ASP324 4.9 66.6 1.0
OD1 D:ASP324 4.9 58.0 1.0
CE D:MET193 4.9 62.2 1.0

Zinc binding site 9 out of 16 in 3mkv

Go back to Zinc Binding Sites List in 3mkv
Zinc binding site 9 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn425

b:63.7
occ:1.00
OD1 E:ASP324 2.1 68.4 1.0
NE2 E:HIS63 2.1 50.6 1.0
NE2 E:HIS65 2.2 58.2 1.0
OQ2 E:KCX191 2.3 59.1 1.0
CG E:ASP324 2.9 57.4 1.0
CE1 E:HIS65 3.0 58.8 1.0
CE1 E:HIS63 3.1 52.6 1.0
CD2 E:HIS63 3.1 46.7 1.0
CX E:KCX191 3.2 63.4 1.0
CD2 E:HIS65 3.2 51.2 1.0
OD2 E:ASP324 3.2 63.2 1.0
ZN E:ZN426 3.3 68.2 1.0
OQ1 E:KCX191 3.5 58.8 1.0
O E:HOH489 3.6 65.8 1.0
ND1 E:HIS63 4.2 51.5 1.0
ND1 E:HIS65 4.2 56.4 1.0
CB E:ASP324 4.2 54.6 1.0
NE2 E:HIS252 4.2 67.9 1.0
CG E:HIS63 4.3 53.1 1.0
CE1 E:HIS252 4.3 66.8 1.0
CG E:HIS65 4.3 50.8 1.0
NZ E:KCX191 4.3 58.0 1.0
O4 E:SO4428 4.6 51.2 0.5
CB E:ALA106 4.6 54.9 1.0
CA E:ASP324 5.0 50.8 1.0

Zinc binding site 10 out of 16 in 3mkv

Go back to Zinc Binding Sites List in 3mkv
Zinc binding site 10 out of 16 in the Crystal Structure of Amidohydrolase EAJ56179


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 Amidohydrolase EAJ56179 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn426

b:68.2
occ:1.00
NE2 E:HIS252 2.2 67.9 1.0
OQ1 E:KCX191 2.2 58.8 1.0
ND1 E:HIS232 2.2 61.7 1.0
O4 E:SO4428 2.9 51.2 0.5
CX E:KCX191 3.0 63.4 1.0
CE1 E:HIS232 3.0 63.4 1.0
OQ2 E:KCX191 3.1 59.1 1.0
CD2 E:HIS252 3.1 65.6 1.0
CE1 E:HIS252 3.2 66.8 1.0
ZN E:ZN425 3.3 63.7 1.0
CG E:HIS232 3.4 57.0 1.0
CB E:HIS232 3.8 54.1 1.0
CE1 E:HIS63 4.1 52.6 1.0
NE2 E:HIS63 4.1 50.6 1.0
O E:HOH489 4.1 65.8 1.0
NE2 E:HIS232 4.2 58.1 1.0
NZ E:KCX191 4.2 58.0 1.0
ND1 E:HIS252 4.3 70.1 1.0
S E:SO4428 4.3 69.2 0.5
CG E:HIS252 4.3 68.7 1.0
OD2 E:ASP324 4.4 63.2 1.0
CD2 E:HIS232 4.4 57.3 1.0
CA E:HIS232 4.5 55.1 1.0
NE2 E:HIS140 4.7 85.3 1.0
O1 E:SO4428 4.7 58.6 0.5
O3 E:SO4428 4.8 60.9 0.5
CD2 E:HIS140 4.8 81.2 1.0
OD1 E:ASP324 4.8 68.4 1.0
SD E:MET193 4.8 48.6 1.0
CE E:KCX191 4.8 52.7 1.0
CG E:ASP324 4.9 57.4 1.0

Reference:

D.F.Xiang, Y.Patskovsky, C.Xu, A.A.Fedorov, E.V.Fedorov, A.A.Sisco, J.M.Sauder, S.K.Burley, S.C.Almo, F.M.Raushel. Functional Identification and Structure Determination of Two Novel Prolidases From COG1228 in the Amidohydrolase Superfamily . Biochemistry V. 49 6791 2010.
ISSN: ISSN 0006-2960
PubMed: 20604542
DOI: 10.1021/BI100897U
Page generated: Wed Dec 16 04:35:32 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy