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Manganese in PDB 5xsn: The Catalytic Domain of Gdpp with C-Di-Amp

Protein crystallography data

The structure of The Catalytic Domain of Gdpp with C-Di-Amp, PDB code: 5xsn was solved by F.Wang, L.Gu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.10 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.620, 117.465, 126.879, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 23.6

Manganese Binding Sites:

The binding sites of Manganese atom in the The Catalytic Domain of Gdpp with C-Di-Amp (pdb code 5xsn). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the The Catalytic Domain of Gdpp with C-Di-Amp, PDB code: 5xsn:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 5xsn

Go back to Manganese Binding Sites List in 5xsn
Manganese binding site 1 out of 4 in the The Catalytic Domain of Gdpp with C-Di-Amp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Catalytic Domain of Gdpp with C-Di-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn701

b:46.0
occ:1.00
OD2 A:ASP349 2.1 40.7 1.0
O A:HOH815 2.3 44.4 1.0
NE2 A:HIS442 2.4 39.3 1.0
OD2 A:ASP497 2.4 35.4 1.0
OD1 A:ASP418 2.5 35.1 1.0
O A:HOH855 3.1 44.4 1.0
CG A:ASP349 3.2 37.5 1.0
CG A:ASP418 3.2 37.9 1.0
CD2 A:HIS442 3.3 36.2 1.0
OD2 A:ASP418 3.3 43.9 1.0
CE1 A:HIS442 3.4 36.8 1.0
CG A:ASP497 3.4 38.4 1.0
MN A:MN702 3.5 75.2 1.0
CB A:ASP349 3.5 36.3 1.0
OD1 A:ASP497 3.7 35.0 1.0
NE2 A:HIS443 4.0 54.3 1.0
CE1 A:HIS443 4.0 45.9 1.0
OD1 A:ASP349 4.3 37.0 1.0
OG1 A:THR465 4.3 36.2 1.0
N A:THR465 4.3 32.4 1.0
CG A:HIS442 4.5 38.4 1.0
ND1 A:HIS442 4.5 37.4 1.0
CA A:SER464 4.5 34.4 1.0
CB A:ASP418 4.6 37.9 1.0
CB A:SER464 4.7 33.6 1.0
CB A:ASP497 4.8 31.2 1.0
C A:SER464 5.0 31.8 1.0
CA A:ASP349 5.0 31.0 1.0

Manganese binding site 2 out of 4 in 5xsn

Go back to Manganese Binding Sites List in 5xsn
Manganese binding site 2 out of 4 in the The Catalytic Domain of Gdpp with C-Di-Amp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Catalytic Domain of Gdpp with C-Di-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn702

b:75.2
occ:1.00
O A:HOH815 2.4 44.4 1.0
OD2 A:ASP418 2.4 43.9 1.0
OD2 A:ASP347 2.5 48.1 1.0
NE2 A:HIS343 2.7 41.8 1.0
OD1 A:ASP347 3.0 44.1 1.0
CG A:ASP347 3.1 43.3 1.0
CG A:ASP418 3.4 37.9 1.0
MN A:MN701 3.5 46.0 1.0
CE1 A:HIS343 3.5 38.2 1.0
CD2 A:HIS343 3.7 42.0 1.0
O A:HOH855 3.7 44.4 1.0
OD1 A:ASP418 3.8 35.1 1.0
CB A:ASP349 4.5 36.3 1.0
CB A:ASP347 4.6 35.1 1.0
O A:ASP418 4.6 33.5 1.0
ND1 A:HIS343 4.7 39.5 1.0
CB A:ASP418 4.7 37.9 1.0
N A:ALA350 4.8 32.2 1.0
CG A:HIS343 4.8 37.1 1.0
OD2 A:ASP349 4.8 40.7 1.0
OD1 A:ASP497 4.8 35.0 1.0
CB A:ALA350 5.0 39.0 1.0

Manganese binding site 3 out of 4 in 5xsn

Go back to Manganese Binding Sites List in 5xsn
Manganese binding site 3 out of 4 in the The Catalytic Domain of Gdpp with C-Di-Amp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Catalytic Domain of Gdpp with C-Di-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn701

b:46.4
occ:1.00
OD2 B:ASP349 2.3 32.2 1.0
OD1 B:ASP418 2.3 34.0 1.0
OD2 B:ASP497 2.4 37.9 1.0
NE2 B:HIS442 2.5 38.8 1.0
OD2 B:ASP418 2.9 37.6 1.0
CG B:ASP418 2.9 36.4 1.0
CG B:ASP349 3.3 34.2 1.0
CD2 B:HIS442 3.4 33.1 1.0
CG B:ASP497 3.4 39.4 1.0
CE1 B:HIS442 3.5 39.2 1.0
MN B:MN702 3.6 80.1 1.0
CB B:ASP349 3.7 31.8 1.0
OD1 B:ASP497 3.8 35.9 1.0
NE2 B:HIS443 4.3 55.5 1.0
CE1 B:HIS443 4.3 48.3 1.0
N B:THR465 4.4 32.9 1.0
OG1 B:THR465 4.4 31.8 1.0
CB B:ASP418 4.4 31.0 1.0
CA B:SER464 4.4 31.1 1.0
OD1 B:ASP349 4.4 32.3 1.0
ND1 B:HIS442 4.6 33.1 1.0
CG B:HIS442 4.6 32.7 1.0
CB B:SER464 4.7 31.8 1.0
CB B:ASP497 4.8 34.4 1.0
C B:SER464 4.9 35.8 1.0

Manganese binding site 4 out of 4 in 5xsn

Go back to Manganese Binding Sites List in 5xsn
Manganese binding site 4 out of 4 in the The Catalytic Domain of Gdpp with C-Di-Amp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Catalytic Domain of Gdpp with C-Di-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn702

b:80.1
occ:1.00
OD2 B:ASP347 2.5 47.8 1.0
OD2 B:ASP418 2.5 37.6 1.0
OD1 B:ASP347 2.5 40.4 1.0
NE2 B:HIS343 2.7 42.0 1.0
CG B:ASP347 2.8 40.7 1.0
CD2 B:HIS343 3.5 39.4 1.0
MN B:MN701 3.6 46.4 1.0
CG B:ASP418 3.6 36.4 1.0
CE1 B:HIS343 3.6 40.9 1.0
OD1 B:ASP418 4.2 34.0 1.0
CB B:ASP347 4.3 37.6 1.0
N B:ALA350 4.6 35.7 1.0
CB B:ASP349 4.6 31.8 1.0
CG B:HIS343 4.7 41.4 1.0
ND1 B:HIS343 4.7 46.3 1.0
CB B:ASP418 4.7 31.0 1.0
OD1 B:ASP497 4.7 35.9 1.0
CB B:ALA350 4.8 35.5 1.0
N B:ASP347 4.8 39.1 1.0
O B:HOH856 4.8 37.8 1.0
O B:ASP418 4.8 38.3 1.0
OD2 B:ASP349 4.9 32.2 1.0

Reference:

F.Wang, Q.He, K.Su, T.Wei, S.Xu, L.Gu. Structural and Biochemical Characterization of the Catalytic Domains of Gdpp Reveals A Unified Hydrolysis Mechanism For the Dhh/DHHA1 Phosphodiesterase Biochem. J. V. 475 191 2018.
ISSN: ESSN 1470-8728
PubMed: 29203646
DOI: 10.1042/BCJ20170739
Page generated: Tue Dec 15 04:49:08 2020

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