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Manganese in PDB 4fcx: S.Pombe MRE11 Apoenzym

Protein crystallography data

The structure of S.Pombe MRE11 Apoenzym, PDB code: 4fcx was solved by C.B.Schiller, K.Lammens, K.P.Hopfner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.84 / 3.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 76.408, 82.262, 164.296, 90.00, 90.00, 90.00
R / Rfree (%) 22.7 / 28.6

Manganese Binding Sites:

The binding sites of Manganese atom in the S.Pombe MRE11 Apoenzym (pdb code 4fcx). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the S.Pombe MRE11 Apoenzym, PDB code: 4fcx:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 4fcx

Go back to Manganese Binding Sites List in 4fcx
Manganese binding site 1 out of 4 in the S.Pombe MRE11 Apoenzym


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of S.Pombe MRE11 Apoenzym within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:49.9
occ:1.00
OD2 B:ASP25 2.2 59.1 1.0
NE2 B:HIS252 2.4 58.9 1.0
OD1 B:ASP65 2.5 58.2 1.0
NE2 B:HIS27 2.5 58.9 1.0
MN B:MN502 3.2 50.0 1.0
CD2 B:HIS252 3.2 57.9 1.0
CG B:ASP65 3.4 63.4 1.0
CG B:ASP25 3.4 61.7 1.0
CE1 B:HIS252 3.4 62.9 1.0
CE1 B:HIS27 3.4 59.3 1.0
CD2 B:HIS27 3.5 59.0 1.0
O B:HIS250 3.6 56.5 1.0
CB B:ASP65 3.8 62.1 1.0
CB B:ASP25 4.0 58.9 1.0
CG B:HIS252 4.4 57.1 1.0
OD1 B:ASP25 4.4 64.1 1.0
OD2 B:ASP65 4.5 67.3 1.0
ND1 B:HIS252 4.5 59.6 1.0
NE2 B:HIS222 4.5 59.5 1.0
C B:HIS250 4.5 57.6 1.0
ND1 B:HIS27 4.6 59.9 1.0
CE1 B:HIS222 4.6 61.3 1.0
CG B:HIS27 4.6 62.3 1.0
CA B:HIS250 4.7 58.1 1.0
OD1 B:ASN133 4.7 73.3 1.0
CA B:ASP25 5.0 56.8 1.0

Manganese binding site 2 out of 4 in 4fcx

Go back to Manganese Binding Sites List in 4fcx
Manganese binding site 2 out of 4 in the S.Pombe MRE11 Apoenzym


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of S.Pombe MRE11 Apoenzym within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn502

b:50.0
occ:1.00
OD1 B:ASP65 2.3 58.2 1.0
NE2 B:HIS222 2.5 59.5 1.0
ND2 B:ASN133 2.5 70.8 1.0
ND1 B:HIS250 2.5 57.6 1.0
OD1 B:ASN133 2.8 73.3 1.0
CG B:ASN133 3.0 71.9 1.0
MN B:MN501 3.2 49.9 1.0
CE1 B:HIS250 3.2 60.2 1.0
CD2 B:HIS222 3.3 61.0 1.0
CG B:ASP65 3.3 63.4 1.0
CE1 B:HIS222 3.4 61.3 1.0
CG B:HIS250 3.6 56.2 1.0
CA B:HIS250 3.7 58.1 1.0
OD2 B:ASP65 3.9 67.3 1.0
CB B:HIS250 4.0 57.2 1.0
OD2 B:ASP25 4.0 59.1 1.0
O B:HIS250 4.0 56.5 1.0
C B:HIS250 4.3 57.6 1.0
NE2 B:HIS250 4.4 62.7 1.0
CG B:HIS222 4.4 62.4 1.0
ND1 B:HIS222 4.4 62.1 1.0
N B:ASN133 4.5 63.4 1.0
CB B:ASP65 4.5 62.1 1.0
CB B:ASN133 4.5 70.8 1.0
CD2 B:HIS250 4.6 59.0 1.0
N B:HIS250 4.6 56.4 1.0

Manganese binding site 3 out of 4 in 4fcx

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Manganese binding site 3 out of 4 in the S.Pombe MRE11 Apoenzym


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of S.Pombe MRE11 Apoenzym within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:58.0
occ:1.00
OD2 A:ASP65 2.2 59.5 1.0
CE1 A:HIS222 2.5 56.9 1.0
ND1 A:HIS250 2.5 52.7 1.0
ND2 A:ASN133 2.9 59.8 1.0
NE2 A:HIS222 3.1 55.6 1.0
MN A:MN502 3.1 64.0 1.0
CG A:ASP65 3.2 60.8 1.0
CE1 A:HIS250 3.3 55.3 1.0
OD1 A:ASP65 3.6 61.6 1.0
CG A:HIS250 3.6 53.4 1.0
ND1 A:HIS222 3.6 58.6 1.0
CG A:ASN133 4.0 73.1 1.0
CB A:HIS250 4.0 55.8 1.0
OD2 A:ASP25 4.0 61.0 1.0
CA A:HIS250 4.0 56.9 1.0
OD1 A:ASN133 4.3 75.9 1.0
CD2 A:HIS222 4.4 57.3 1.0
NE2 A:HIS250 4.5 54.1 1.0
CB A:ASP65 4.5 59.8 1.0
O A:HIS250 4.5 54.4 1.0
CD2 A:HIS250 4.6 51.7 1.0
CG A:HIS222 4.6 57.8 1.0
N A:ASN133 4.8 62.6 1.0
C A:HIS250 4.8 51.5 1.0

Manganese binding site 4 out of 4 in 4fcx

Go back to Manganese Binding Sites List in 4fcx
Manganese binding site 4 out of 4 in the S.Pombe MRE11 Apoenzym


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of S.Pombe MRE11 Apoenzym within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn502

b:64.0
occ:1.00
OD2 A:ASP65 2.3 59.5 1.0
OD2 A:ASP25 2.3 61.0 1.0
NE2 A:HIS252 2.4 54.8 1.0
NE2 A:HIS27 2.5 55.1 1.0
MN A:MN501 3.1 58.0 1.0
CD2 A:HIS252 3.2 57.1 1.0
CG A:ASP65 3.3 60.8 1.0
CE1 A:HIS27 3.5 54.4 1.0
CD2 A:HIS27 3.5 58.2 1.0
CG A:ASP25 3.5 61.2 1.0
CE1 A:HIS252 3.5 57.8 1.0
CB A:ASP65 3.7 59.8 1.0
CB A:ASP25 4.1 59.4 1.0
OD1 A:ASP65 4.4 61.6 1.0
CG A:HIS252 4.4 55.1 1.0
OD1 A:ASP25 4.5 65.9 1.0
ND1 A:HIS252 4.6 58.7 1.0
NE2 A:HIS222 4.6 55.6 1.0
ND1 A:HIS27 4.6 54.9 1.0
CG A:HIS27 4.6 59.2 1.0
CA A:HIS250 4.8 56.9 1.0
CE1 A:HIS222 4.8 56.9 1.0
ND1 A:HIS250 4.9 52.7 1.0
O A:HIS250 4.9 54.4 1.0

Reference:

C.B.Schiller, K.Lammens, I.Guerini, B.Coordes, H.Feldmann, F.Schlauderer, C.Mockel, A.Schele, K.Strasser, S.P.Jackson, K.P.Hopfner. Structure of MRE11-NBS1 Complex Yields Insights Into Ataxia-Telangiectasia-Like Disease Mutations and Dna Damage Signaling. Nat.Struct.Mol.Biol. V. 19 693 2012.
ISSN: ISSN 1545-9993
PubMed: 22705791
DOI: 10.1038/NSMB.2323
Page generated: Tue Dec 15 04:20:38 2020

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