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Manganese in PDB 4mr0: Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae

Protein crystallography data

The structure of Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae, PDB code: 4mr0 was solved by K.Ponnuraj, D.S.J.Beulin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 60.590, 126.080, 63.480, 90.00, 99.60, 90.00
R / Rfree (%) 20.4 / 22.2

Other elements in 4mr0:

The structure of Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Calcium (Ca) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae (pdb code 4mr0). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae, PDB code: 4mr0:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Manganese binding site 1 out of 8 in 4mr0

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Manganese binding site 1 out of 8 in the Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn704

b:19.5
occ:1.00
 OE2 A:GLU198 2.2 18.6 1.0
O A:THR236 2.2 16.0 1.0
O A:HOH1026 2.3 21.7 1.0
NE2 A:HIS225 2.3 15.5 1.0
O A:HOH974 2.4 19.2 1.0
O A:HOH1027 2.4 14.8 1.0
CD2 A:HIS225 3.2 14.9 1.0
CD A:GLU198 3.2 19.4 1.0
C A:THR236 3.3 18.1 1.0
CE1 A:HIS225 3.4 15.0 1.0
OE1 A:GLU198 3.5 19.1 1.0
CA A:THR236 3.8 16.7 1.0
OD2 A:ASP237 4.3 23.1 1.0
O A:HOH846 4.3 22.9 1.0
O A:PHE235 4.4 18.0 1.0
CG A:HIS225 4.4 16.4 1.0
ND1 A:HIS225 4.4 15.7 1.0
CD1 A:PHE235 4.4 17.3 1.0
N A:ASP237 4.5 18.7 1.0
CD1 A:ILE222 4.6 19.9 1.0
CG A:GLU198 4.6 16.5 1.0
N A:THR236 4.6 17.4 1.0
CG A:ASP237 4.6 22.2 1.0
CE1 A:PHE235 4.6 17.6 1.0
OD1 A:ASP237 4.8 23.0 1.0
C A:PHE235 4.8 17.8 1.0
CA A:ASP237 4.9 19.1 1.0
CB A:THR236 5.0 18.2 1.0

Manganese binding site 2 out of 8 in 4mr0

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Manganese binding site 2 out of 8 in the Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn705

b:23.9
occ:1.00
 O A:GLY350 2.2 17.0 1.0
OE1 A:GLN342 2.2 15.1 1.0
OE2 A:GLU344 2.3 19.9 1.0
OE1 A:GLN307 2.3 16.5 1.0
OE1 A:GLU344 2.6 19.1 1.0
CD A:GLU344 2.8 18.2 1.0
MN A:MN707 3.1 50.1 1.0
CD A:GLN342 3.1 18.8 1.0
C A:GLY350 3.3 18.0 1.0
CD A:GLN307 3.4 18.6 1.0
O A:HOH1042 3.4 54.8 1.0
NE2 A:GLN342 3.6 18.1 1.0
CG A:GLN307 3.9 16.8 1.0
O A:HOH878 3.9 30.3 1.0
CA A:GLY350 3.9 18.3 1.0
CG A:GLU344 4.3 17.8 1.0
CG A:GLN342 4.3 15.9 1.0
N A:PHE351 4.4 15.4 1.0
NE2 A:HIS304 4.4 18.8 1.0
CB A:GLN307 4.4 15.6 1.0
CD2 A:HIS304 4.5 18.5 1.0
NE2 A:GLN307 4.5 16.5 1.0
O A:HOH1040 4.5 37.7 1.0
O A:HOH903 4.7 14.1 1.0
CA A:PHE351 4.7 15.0 1.0
O A:HOH1076 4.8 47.8 1.0
CD1 A:PHE351 4.8 14.9 1.0
CB A:GLN342 4.9 14.8 1.0

Manganese binding site 3 out of 8 in 4mr0

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Manganese binding site 3 out of 8 in the Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn706

b:46.3
occ:1.00
 O A:HOH1028 2.0 31.2 1.0
O A:HOH1030 2.1 44.4 1.0
O A:HOH1029 2.1 37.8 1.0
O A:HOH1041 2.4 42.2 1.0
NE2 A:HIS440 3.5 26.9 1.0
N A:GLY379 3.7 22.6 1.0
O A:HOH978 3.9 26.1 1.0
N A:LEU326 4.0 26.0 1.0
CA A:SER378 4.1 25.2 1.0
CA A:ALA325 4.1 22.8 1.0
CE1 A:HIS440 4.2 25.9 1.0
CB A:SER378 4.3 25.6 1.0
CD1 A:LEU263 4.3 26.5 1.0
O A:GLN324 4.4 20.2 1.0
C A:SER378 4.4 23.4 1.0
CD2 A:HIS440 4.6 26.0 1.0
O A:LEU326 4.6 31.7 1.0
C A:ALA325 4.6 24.5 1.0
CA A:GLY379 4.7 21.8 1.0
CB A:ALA325 4.7 22.1 1.0
CG A:LEU263 4.7 26.3 1.0
O A:LYS377 4.8 28.2 1.0
CG1 A:VAL439 4.9 32.6 1.0

Manganese binding site 4 out of 8 in 4mr0

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Manganese binding site 4 out of 8 in the Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn707

b:50.1
occ:1.00
 O A:HOH1040 2.1 37.7 1.0
O A:HOH1076 2.2 47.8 1.0
O A:HOH1042 2.2 54.8 1.0
MN A:MN705 3.1 23.9 1.0
O A:HOH878 3.5 30.3 1.0
O A:GLY350 3.7 17.0 1.0
OE1 A:GLN342 3.7 15.1 1.0
NE2 A:GLN342 3.8 18.1 1.0
NE2 A:HIS304 3.8 18.8 1.0
O A:HOH998 3.9 31.9 1.0
CA A:GLY350 3.9 18.3 1.0
O A:HOH975 4.1 32.8 1.0
C A:GLY350 4.2 18.0 1.0
CD A:GLN342 4.2 18.8 1.0
OE1 A:GLU344 4.3 19.1 1.0
NE2 A:HIS388 4.3 22.4 1.0
CE1 A:HIS388 4.4 20.8 1.0
O A:LYS349 4.4 19.6 1.0
OE1 A:GLN307 4.5 16.5 1.0
CD2 A:HIS304 4.6 18.5 1.0
CE1 A:HIS304 4.7 19.4 1.0

Manganese binding site 5 out of 8 in 4mr0

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Manganese binding site 5 out of 8 in the Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn704

b:18.4
occ:1.00
 O B:THR236 2.2 16.4 1.0
OE1 B:GLU198 2.2 20.2 1.0
O B:HOH1001 2.3 19.6 1.0
O B:HOH1007 2.3 17.4 1.0
O B:HOH1009 2.3 23.5 1.0
NE2 B:HIS225 2.4 15.6 1.0
CD2 B:HIS225 3.2 17.4 1.0
CD B:GLU198 3.2 21.6 1.0
C B:THR236 3.2 17.7 1.0
CE1 B:HIS225 3.4 16.0 1.0
OE2 B:GLU198 3.5 19.1 1.0
CA B:THR236 3.7 18.7 1.0
O B:HOH970 4.1 34.7 1.0
OD1 B:ASP237 4.3 22.1 1.0
O B:HOH963 4.3 26.0 1.0
O B:PHE235 4.3 19.2 1.0
CG B:HIS225 4.4 17.7 1.0
N B:ASP237 4.4 18.5 1.0
CD2 B:PHE235 4.4 18.6 1.0
ND1 B:HIS225 4.5 17.4 1.0
CD1 B:ILE222 4.5 20.6 1.0
CG B:GLU198 4.5 18.6 1.0
N B:THR236 4.5 17.9 1.0
CE2 B:PHE235 4.6 20.1 1.0
CG B:ASP237 4.7 20.0 1.0
C B:PHE235 4.8 18.7 1.0
CA B:ASP237 4.8 20.4 1.0
CB B:THR236 4.9 19.3 1.0
OD2 B:ASP237 4.9 20.0 1.0

Manganese binding site 6 out of 8 in 4mr0

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Manganese binding site 6 out of 8 in the Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn705

b:28.1
occ:1.00
 O B:GLY350 2.3 20.6 1.0
OE1 B:GLN307 2.3 16.9 1.0
OE1 B:GLN342 2.3 15.6 1.0
OE2 B:GLU344 2.4 22.9 1.0
OE1 B:GLU344 2.6 21.4 1.0
CD B:GLU344 2.8 21.4 1.0
CD B:GLN342 3.2 18.2 1.0
MN B:MN707 3.3 50.1 1.0
CD B:GLN307 3.3 19.0 1.0
C B:GLY350 3.4 22.6 1.0
O B:HOH1065 3.7 33.4 1.0
NE2 B:GLN342 3.8 21.0 1.0
O B:HOH1031 3.8 46.6 1.0
CG B:GLN307 3.9 14.5 1.0
CA B:GLY350 4.0 24.1 1.0
CG B:GLU344 4.3 20.3 1.0
CG B:GLN342 4.3 17.9 1.0
CB B:GLN307 4.4 14.8 1.0
NE2 B:HIS304 4.4 17.4 1.0
CD2 B:HIS304 4.4 20.0 1.0
N B:PHE351 4.4 20.4 1.0
NE2 B:GLN307 4.5 15.7 1.0
O B:HOH816 4.5 19.6 1.0
CA B:PHE351 4.7 19.3 1.0
CD1 B:PHE351 4.8 14.2 1.0
CB B:GLN342 4.9 15.7 1.0

Manganese binding site 7 out of 8 in 4mr0

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Manganese binding site 7 out of 8 in the Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn706

b:39.8
occ:1.00
 O B:HOH1010 2.0 29.0 1.0
O B:HOH1012 2.0 42.5 1.0
O B:HOH1011 2.1 30.5 1.0
O B:HOH1013 2.4 30.7 1.0
NE2 B:HIS440 3.4 21.8 1.0
O B:HOH962 3.8 23.6 1.0
N B:GLY379 3.9 20.9 1.0
N B:LEU326 3.9 25.1 1.0
CA B:ALA325 4.0 22.7 1.0
CE1 B:HIS440 4.1 21.0 1.0
CD1 B:LEU263 4.1 26.1 1.0
CA B:SER378 4.3 22.7 1.0
O B:GLN324 4.3 20.0 1.0
CB B:SER378 4.4 23.7 1.0
CD2 B:HIS440 4.4 22.0 1.0
O B:LEU326 4.4 28.6 1.0
C B:ALA325 4.5 24.2 1.0
CB B:ALA325 4.6 22.6 1.0
C B:SER378 4.6 22.0 1.0
O B:HOH924 4.6 24.8 1.0
CG B:LEU263 4.7 26.0 1.0
O B:HOH859 4.7 46.2 1.0
CA B:GLY379 4.8 21.6 1.0
CA B:LEU326 4.9 26.8 1.0
O B:LYS377 5.0 26.0 1.0

Manganese binding site 8 out of 8 in 4mr0

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Manganese binding site 8 out of 8 in the Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn707

b:50.1
occ:1.00
 O B:HOH1031 2.3 46.6 1.0
MN B:MN705 3.3 28.1 1.0
O B:HOH1065 3.5 33.4 1.0
NE2 B:HIS304 3.6 17.4 1.0
OE1 B:GLN342 3.7 15.6 1.0
NE2 B:GLN342 3.8 21.0 1.0
O B:GLY350 3.9 20.6 1.0
NE2 B:HIS388 4.0 25.1 1.0
CE1 B:HIS388 4.1 24.3 1.0
O B:HOH1032 4.2 39.5 1.0
CD B:GLN342 4.2 18.2 1.0
CA B:GLY350 4.2 24.1 1.0
CD2 B:HIS304 4.4 20.0 1.0
CE1 B:HIS304 4.5 20.6 1.0
C B:GLY350 4.5 22.6 1.0
OE1 B:GLU344 4.5 21.4 1.0
OE1 B:GLN307 4.6 16.9 1.0
O B:LYS349 4.7 29.2 1.0
O B:HOH816 4.9 19.6 1.0

Reference:

D.S.J.Beulin, M.Yamaguchi, S.Kawabata, K.Ponnuraj. Crystal Structure of Pfba, A Surface Adhesin of Streptococcus Pneumoniae, Provides Hints Into Its Interaction with Fibronectin Int.J.Biol.Macromol. V. 64C 168 2013.
ISSN: ISSN 0141-8130
PubMed: 24321492
DOI: 10.1016/J.IJBIOMAC.2013.11.035
Page generated: Tue Dec 15 04:24:41 2020

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