Atomistry » Manganese » PDB 1yw7-2a2t » 1zm8
Atomistry »
  Manganese »
    PDB 1yw7-2a2t »
      1zm8 »

Manganese in PDB 1zm8: Apo Crystal Structure of Nuclease A From Anabaena Sp.

Protein crystallography data

The structure of Apo Crystal Structure of Nuclease A From Anabaena Sp., PDB code: 1zm8 was solved by M.Ghosh, G.Meiss, A.Pingoud, R.E.London, L.C.Pedersen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.87 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.690, 66.682, 81.730, 90.00, 90.00, 90.00
R / Rfree (%) 21.2 / 25.6

Other elements in 1zm8:

The structure of Apo Crystal Structure of Nuclease A From Anabaena Sp. also contains other interesting chemical elements:

Sodium (Na) 1 atom

Manganese Binding Sites:

The binding sites of Manganese atom in the Apo Crystal Structure of Nuclease A From Anabaena Sp. (pdb code 1zm8). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Apo Crystal Structure of Nuclease A From Anabaena Sp., PDB code: 1zm8:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 1zm8

Go back to Manganese Binding Sites List in 1zm8
Manganese binding site 1 out of 3 in the Apo Crystal Structure of Nuclease A From Anabaena Sp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Apo Crystal Structure of Nuclease A From Anabaena Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn275

b:37.6
occ:1.00
OD1 A:ASN155 2.0 38.1 1.0
O A:HOH282 2.1 31.3 1.0
O4 A:SO4278 2.1 59.5 1.0
O A:HOH281 2.2 30.4 1.0
O A:HOH284 2.3 29.6 1.0
O A:HOH283 2.4 35.6 1.0
CG A:ASN155 3.2 36.7 1.0
S A:SO4278 3.4 61.0 1.0
ND2 A:ASN155 3.7 35.6 1.0
O2 A:SO4278 3.8 60.0 1.0
O3 A:SO4278 3.8 59.9 1.0
N A:HIS124 4.0 34.8 1.0
O A:HOH300 4.1 32.0 1.0
OE1 A:GLU163 4.1 34.6 1.0
OE2 A:GLU163 4.1 32.2 1.0
ND1 A:HIS124 4.3 34.0 1.0
OE1 A:GLN150 4.3 42.7 1.0
O A:ASN155 4.4 37.1 1.0
CB A:ASN155 4.4 36.3 1.0
CD1 A:TRP159 4.5 34.6 1.0
CB A:HIS124 4.5 33.5 1.0
CA A:GLY123 4.5 36.8 1.0
CD A:GLU163 4.5 32.6 1.0
O A:HIS124 4.5 32.1 1.0
O1 A:SO4278 4.5 63.3 1.0
CA A:ASN155 4.7 37.3 1.0
C A:GLY123 4.7 36.9 1.0
CA A:HIS124 4.8 33.4 1.0
C A:ASN155 4.8 37.9 1.0
CG A:HIS124 4.8 33.5 1.0
NE1 A:TRP159 4.9 34.3 1.0

Manganese binding site 2 out of 3 in 1zm8

Go back to Manganese Binding Sites List in 1zm8
Manganese binding site 2 out of 3 in the Apo Crystal Structure of Nuclease A From Anabaena Sp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Apo Crystal Structure of Nuclease A From Anabaena Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn276

b:39.7
occ:1.00
OD1 A:ASP246 2.1 27.7 0.7
OE1 A:GLU249 2.1 35.4 1.0
OE1 A:GLU269 2.1 39.8 1.0
O A:HOH285 2.4 46.2 1.0
CD A:GLU249 3.1 36.1 1.0
CD A:GLU269 3.3 43.0 1.0
CG A:ASP246 3.3 29.8 0.7
OE2 A:GLU249 3.5 34.3 1.0
CB A:GLU269 3.6 43.2 1.0
MN A:MN277 3.7 42.9 1.0
CG A:GLU269 4.0 41.9 1.0
OD2 A:ASP246 4.0 30.4 0.7
O A:HOH325 4.1 39.3 1.0
OE2 A:GLU269 4.3 41.1 1.0
CA A:ASP246 4.3 32.3 1.0
CB A:ASP246 4.4 30.8 0.7
CG A:GLU249 4.4 35.0 1.0
N A:ASP246 4.7 32.7 1.0
CA A:GLU269 4.9 43.9 1.0
OE1 A:GLN265 5.0 36.8 1.0

Manganese binding site 3 out of 3 in 1zm8

Go back to Manganese Binding Sites List in 1zm8
Manganese binding site 3 out of 3 in the Apo Crystal Structure of Nuclease A From Anabaena Sp.


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Apo Crystal Structure of Nuclease A From Anabaena Sp. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn277

b:42.9
occ:1.00
OD1 A:ASP255 2.4 36.4 1.0
OE2 A:GLU249 2.4 34.3 1.0
O A:PHE256 2.5 32.8 1.0
OE1 A:GLN265 2.5 36.8 1.0
OE1 A:GLU269 2.5 39.8 1.0
OE2 A:GLU269 2.7 41.1 1.0
CD A:GLU269 2.9 43.0 1.0
CD A:GLU249 3.5 36.1 1.0
C A:PHE256 3.6 33.1 1.0
N A:PHE256 3.6 30.9 1.0
CG A:ASP255 3.6 34.9 1.0
CD A:GLN265 3.6 39.0 1.0
MN A:MN276 3.7 39.7 1.0
OE1 A:GLU249 3.8 35.4 1.0
C A:ASP255 4.0 31.6 1.0
CA A:PHE256 4.1 30.9 1.0
CA A:ASP255 4.3 31.9 1.0
CG A:GLN265 4.4 41.2 1.0
OD2 A:ASP255 4.4 33.8 1.0
CG A:GLU269 4.4 41.9 1.0
CB A:ASP255 4.5 31.4 1.0
NE2 A:GLN265 4.6 36.3 1.0
O A:HOH310 4.7 35.1 1.0
N A:LEU257 4.7 32.2 1.0
C A:LEU257 4.7 35.5 1.0
O A:ASP255 4.8 30.1 1.0
CB A:PHE256 4.8 31.0 1.0
CG A:GLU249 4.8 35.0 1.0
CB A:GLN265 4.8 42.6 1.0
O A:LEU257 4.8 36.8 1.0
O A:HOH285 4.8 46.2 1.0
CB A:LEU257 4.9 35.0 1.0
N A:SER258 4.9 36.9 1.0

Reference:

M.Ghosh, G.Meiss, A.Pingoud, R.E.London, L.C.Pedersen. Structural Insights Into the Mechanism of Nuclease A, A Beta Beta Alpha Metal Nuclease From Anabaena. J.Biol.Chem. V. 280 27990 2005.
ISSN: ISSN 0021-9258
PubMed: 15897201
DOI: 10.1074/JBC.M501798200
Page generated: Tue Dec 15 03:58:47 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy