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Manganese in PDB 5zyw: The Crystal Structure of Apo-HSMGME1 with MN2+

Protein crystallography data

The structure of The Crystal Structure of Apo-HSMGME1 with MN2+, PDB code: 5zyw was solved by C.Yang, J.Gan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.95 / 2.20
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 67.997, 67.997, 114.841, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 25.2

Manganese Binding Sites:

The binding sites of Manganese atom in the The Crystal Structure of Apo-HSMGME1 with MN2+ (pdb code 5zyw). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the The Crystal Structure of Apo-HSMGME1 with MN2+, PDB code: 5zyw:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 5zyw

Go back to Manganese Binding Sites List in 5zyw
Manganese binding site 1 out of 3 in the The Crystal Structure of Apo-HSMGME1 with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of Apo-HSMGME1 with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:20.6
occ:1.00
O A:HOH554 2.0 17.0 1.0
OD1 A:ASP238 2.1 20.2 1.0
OE2 A:GLU344 2.1 18.0 1.0
O1 A:TLA404 2.2 17.8 1.0
O A:HOH511 2.2 20.2 1.0
O A:HOH528 2.3 19.9 1.0
CD A:GLU344 3.1 18.6 1.0
CG A:ASP238 3.2 21.4 1.0
C1 A:TLA404 3.2 18.2 1.0
OE1 A:GLU344 3.5 19.1 1.0
OD2 A:ASP238 3.7 21.3 1.0
C2 A:TLA404 3.7 18.1 1.0
MN A:MN402 3.9 19.3 1.0
O A:LEU236 4.0 22.6 1.0
CD2 A:HIS180 4.0 20.5 1.0
C3 A:TLA404 4.1 18.3 1.0
OE1 A:GLU223 4.2 25.6 1.0
NE2 A:HIS180 4.2 20.5 1.0
OE2 A:GLU223 4.2 24.6 1.0
OD2 A:ASP251 4.3 20.7 1.0
O11 A:TLA404 4.3 18.6 1.0
O A:HOH588 4.3 20.7 1.0
CG A:GLU344 4.3 18.8 1.0
CB A:ASP238 4.4 22.2 1.0
N A:ASP238 4.5 22.6 1.0
CA A:ASP238 4.5 23.0 1.0
CB A:GLU344 4.6 19.0 1.0
CD A:GLU223 4.6 25.2 1.0
OD1 A:ASP251 4.8 21.5 1.0
O3 A:TLA404 4.8 18.0 1.0
CG A:ASP251 4.9 21.2 1.0
C A:LEU237 4.9 22.3 1.0
CG A:HIS180 5.0 20.9 1.0

Manganese binding site 2 out of 3 in 5zyw

Go back to Manganese Binding Sites List in 5zyw
Manganese binding site 2 out of 3 in the The Crystal Structure of Apo-HSMGME1 with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of Apo-HSMGME1 with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:19.3
occ:1.00
OD2 A:ASP238 2.1 21.3 1.0
O A:TRP252 2.1 19.4 1.0
OD1 A:ASP251 2.2 21.5 1.0
O1 A:TLA404 2.3 17.8 1.0
NE2 A:HIS180 2.3 20.5 1.0
O11 A:TLA404 2.4 18.6 1.0
C1 A:TLA404 2.7 18.2 1.0
CG A:ASP238 3.1 21.4 1.0
CG A:ASP251 3.1 21.2 1.0
C A:TRP252 3.2 19.8 1.0
CE1 A:HIS180 3.3 20.3 1.0
N A:TRP252 3.3 20.6 1.0
CD2 A:HIS180 3.3 20.5 1.0
OD1 A:ASP238 3.4 20.2 1.0
OD2 A:ASP251 3.6 20.7 1.0
CA A:TRP252 3.7 20.6 1.0
MN A:MN401 3.9 20.6 1.0
C A:ASP251 3.9 20.9 1.0
CB A:TRP252 4.1 21.3 1.0
NZ A:LYS253 4.1 18.8 1.0
C2 A:TLA404 4.2 18.1 1.0
CB A:ASP251 4.2 21.3 1.0
CA A:ASP251 4.2 21.6 1.0
O A:HOH554 4.3 17.0 1.0
N A:LYS253 4.4 19.0 1.0
ND1 A:HIS180 4.4 20.2 1.0
CD A:LYS253 4.4 18.9 1.0
CE A:LYS253 4.4 18.8 1.0
CB A:ASP238 4.4 22.2 1.0
CG A:HIS180 4.5 20.9 1.0
O A:ASP251 4.7 20.3 1.0
CA A:LYS253 4.8 18.7 1.0
O3 A:TLA404 4.8 18.0 1.0
CD1 A:TRP252 4.9 22.5 1.0
O A:HOH528 4.9 19.9 1.0
O2 A:TLA404 4.9 18.3 1.0
CG A:TRP252 4.9 22.1 1.0
O A:HOH587 5.0 17.9 1.0
C3 A:TLA404 5.0 18.3 1.0

Manganese binding site 3 out of 3 in 5zyw

Go back to Manganese Binding Sites List in 5zyw
Manganese binding site 3 out of 3 in the The Crystal Structure of Apo-HSMGME1 with MN2+


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of Apo-HSMGME1 with MN2+ within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn403

b:55.3
occ:1.00
OG A:SER343 2.3 18.3 1.0
O A:HOH550 2.4 30.4 1.0
OG1 A:THR134 2.5 18.3 1.0
O A:HOH501 2.7 21.6 1.0
CB A:THR134 3.3 18.5 1.0
CB A:SER343 3.6 19.0 1.0
NZ A:LYS259 3.7 24.4 1.0
N A:GLU344 4.0 18.8 1.0
CA A:SER343 4.2 19.4 1.0
CG2 A:THR134 4.3 18.6 1.0
C A:THR134 4.4 19.8 1.0
N A:ARG135 4.4 21.0 1.0
OXT A:GLU344 4.4 18.9 1.0
CA A:THR134 4.4 19.1 1.0
C A:SER343 4.5 19.3 1.0
O A:HOH564 4.5 29.1 1.0
OG A:SER132 4.6 20.5 1.0
O A:HOH565 4.7 28.7 1.0
O4 A:TLA404 4.7 18.0 1.0
O41 A:TLA404 4.8 18.2 1.0
O A:THR134 4.8 20.8 1.0
OE1 A:GLN138 5.0 26.7 1.0

Reference:

C.Yang, R.Wu, H.Liu, Y.Chen, Y.Gao, X.Chen, Y.Li, J.Ma, J.Li, J.Gan. Structural Insights Into Dna Degradation By Human Mitochondrial Nuclease MGME1 Nucleic Acids Res. V. 46 11075 2018.
ISSN: ESSN 1362-4962
PubMed: 30247721
DOI: 10.1093/NAR/GKY855
Page generated: Sat Aug 16 19:47:16 2025

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