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Magnesium in PDB 1wvm: Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin

Protein crystallography data

The structure of Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin, PDB code: 1wvm was solved by D.Dong, K.Watanabe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.59 / 1.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 123.230, 138.340, 64.880, 90.00, 97.56, 90.00
R / Rfree (%) 19.2 / 20.6

Other elements in 1wvm:

The structure of Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin also contains other interesting chemical elements:

Calcium (Ca) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin (pdb code 1wvm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin, PDB code: 1wvm:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 1wvm

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Magnesium binding site 1 out of 8 in the Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg607

b:21.2
occ:1.00
 CA A:CA604 2.4 17.1 1.0
OG1 A:THR414 2.6 13.4 1.0
O A:GLY415 2.8 13.7 1.0
OD1 A:ASP411 3.0 16.0 1.0
O A:LEU405 3.0 19.1 1.0
N A:LEU405 3.1 17.0 1.0
OD1 A:ASP404 3.1 18.2 1.0
N A:GLY417 3.5 14.2 1.0
C A:TYR416 3.6 15.2 1.0
CA A:GLY417 3.6 13.6 1.0
C A:LEU405 3.7 18.9 1.0
C A:GLY415 3.7 13.2 1.0
CA A:LEU405 3.7 18.1 1.0
CB A:THR414 3.8 12.6 1.0
O A:GLY409 3.8 20.3 1.0
O A:TYR416 3.9 16.7 1.0
CG A:ASP411 3.9 15.7 1.0
CB A:LEU405 4.0 18.3 1.0
O A:THR414 4.1 10.9 1.0
C A:ASP404 4.1 17.6 1.0
C A:THR414 4.1 11.9 1.0
CA A:ASP404 4.2 17.0 1.0
OD2 A:ASP411 4.2 14.0 1.0
CA A:TYR416 4.2 14.7 1.0
CG A:ASP404 4.3 19.4 1.0
N A:TYR416 4.4 12.7 1.0
N A:GLY415 4.4 12.2 1.0
CA A:THR414 4.5 12.1 1.0
N A:ASP411 4.5 15.8 1.0
O A:VAL407 4.7 24.0 1.0
C A:GLY409 4.7 20.1 1.0
CA A:GLY415 4.7 11.8 1.0
CA A:ARG410 4.8 18.2 1.0
CG A:LEU405 4.8 17.4 1.0
N A:SER406 4.8 21.2 1.0
CB A:ASP404 4.9 17.9 1.0
CG2 A:THR414 4.9 13.1 1.0

Magnesium binding site 2 out of 8 in 1wvm

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Magnesium binding site 2 out of 8 in the Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg608

b:10.5
occ:1.00
 O A:VAL174 2.2 9.1 1.0
MG A:MG609 2.3 22.4 1.0
O A:TYR171 2.3 10.3 1.0
OE1 A:GLN195 2.4 12.8 1.0
O A:ALA169 2.4 7.8 1.0
C A:VAL174 3.3 9.3 1.0
C A:TYR171 3.4 10.5 1.0
O A:HOH793 3.5 27.5 1.0
CD A:GLN195 3.6 13.0 1.0
C A:ALA169 3.6 8.9 1.0
N A:TYR171 3.7 10.5 1.0
C A:SER170 3.8 10.6 1.0
CA A:SER170 4.0 10.7 1.0
N A:SER176 4.1 9.0 1.0
N A:VAL174 4.1 9.1 1.0
CA A:VAL174 4.1 9.6 1.0
N A:ASP172 4.2 11.1 1.0
N A:SER170 4.2 9.4 1.0
CA A:TYR171 4.3 9.5 1.0
CB A:SER176 4.3 9.8 1.0
CA A:ASP172 4.3 12.3 1.0
NH1 A:ARG395 4.3 15.1 1.0
CB A:VAL174 4.3 9.4 1.0
O A:SER170 4.4 11.0 1.0
N A:MET175 4.4 8.8 1.0
CB A:GLN195 4.4 10.1 1.0
O A:GLN195 4.4 11.4 1.0
CG A:GLN195 4.4 10.9 1.0
C A:ASP172 4.5 12.4 1.0
OE1 A:GLU197 4.5 16.7 1.0
NE2 A:GLN195 4.5 13.6 1.0
C A:MET175 4.5 11.0 1.0
CA A:MET175 4.5 9.7 1.0
O A:ASP172 4.6 13.0 1.0
CA A:SER176 4.7 9.2 1.0
CA A:ALA169 4.7 7.3 1.0
O A:PRO168 4.9 9.1 1.0

Magnesium binding site 3 out of 8 in 1wvm

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Magnesium binding site 3 out of 8 in the Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg609

b:22.4
occ:1.00
 MG A:MG608 2.3 10.5 1.0
O A:GLN195 2.6 11.4 1.0
OE1 A:GLU197 2.8 16.7 1.0
O A:VAL174 2.9 9.1 1.0
N A:SER176 3.0 9.0 1.0
OE1 A:GLN195 3.3 12.8 1.0
CB A:SER176 3.4 9.8 1.0
O A:HOH793 3.4 27.5 1.0
C A:GLN195 3.7 10.8 1.0
O A:HOH789 3.8 23.5 1.0
O A:ALA169 3.8 7.8 1.0
CA A:SER176 3.8 9.2 1.0
CB A:GLU197 3.9 13.3 1.0
C A:MET175 3.9 11.0 1.0
CA A:MET175 3.9 9.7 1.0
CD A:GLU197 3.9 15.2 1.0
NH1 A:ARG395 4.0 15.1 1.0
C A:VAL174 4.0 9.3 1.0
CA A:GLN195 4.2 11.2 1.0
CB A:GLN195 4.2 10.1 1.0
CD A:GLN195 4.3 13.0 1.0
CG A:GLU197 4.4 15.2 1.0
N A:MET175 4.5 8.8 1.0
O A:TYR171 4.5 10.3 1.0
N A:GLU197 4.5 11.5 1.0
N A:VAL196 4.7 10.4 1.0
OG A:SER176 4.7 10.1 1.0
O A:SER176 4.7 9.4 1.0
CA A:GLU197 4.8 11.2 1.0
C A:SER176 4.8 9.7 1.0
CG A:GLN195 4.9 10.9 1.0
C A:VAL196 4.9 11.1 1.0
C A:ALA169 5.0 8.9 1.0
OE2 A:GLU197 5.0 18.2 1.0
NH1 A:ARG410 5.0 18.3 1.0

Magnesium binding site 4 out of 8 in 1wvm

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Magnesium binding site 4 out of 8 in the Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg610

b:18.5
occ:1.00
 CA B:CA606 2.4 14.2 1.0
OG1 B:THR414 2.7 10.8 1.0
O B:GLY415 2.8 9.6 1.0
OD1 B:ASP404 3.0 12.6 1.0
N B:LEU405 3.1 11.6 1.0
O B:LEU405 3.1 15.6 1.0
OD1 B:ASP411 3.1 13.8 1.0
N B:GLY417 3.4 10.0 1.0
C B:TYR416 3.5 9.4 1.0
CA B:GLY417 3.6 9.8 1.0
O B:GLY409 3.7 18.0 1.0
O B:TYR416 3.7 10.3 1.0
C B:LEU405 3.7 14.7 1.0
C B:GLY415 3.7 9.7 1.0
CA B:LEU405 3.8 12.6 1.0
CB B:THR414 3.8 9.9 1.0
CG B:ASP411 4.0 13.6 1.0
CB B:LEU405 4.0 12.0 1.0
C B:ASP404 4.1 12.3 1.0
O B:THR414 4.1 8.6 1.0
CA B:ASP404 4.1 11.2 1.0
CA B:TYR416 4.1 9.6 1.0
C B:THR414 4.1 9.2 1.0
CG B:ASP404 4.2 16.4 1.0
OD2 B:ASP411 4.3 11.9 1.0
N B:TYR416 4.3 9.9 1.0
N B:GLY415 4.5 9.4 1.0
N B:ASP411 4.6 14.1 1.0
CA B:THR414 4.6 9.4 1.0
O B:VAL407 4.6 21.6 1.0
C B:GLY409 4.7 17.3 1.0
CA B:GLY415 4.8 10.0 1.0
CB B:ASP404 4.8 12.6 1.0
CG B:LEU405 4.8 10.9 1.0
CA B:ARG410 4.8 15.8 1.0
N B:SER406 4.9 17.8 1.0

Magnesium binding site 5 out of 8 in 1wvm

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Magnesium binding site 5 out of 8 in the Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg611

b:7.8
occ:1.00
 O B:VAL174 2.2 7.9 1.0
O B:TYR171 2.3 8.9 1.0
OE1 B:GLN195 2.3 8.5 1.0
O B:ALA169 2.4 7.0 1.0
MG B:MG612 2.4 18.4 1.0
C B:TYR171 3.3 8.7 1.0
C B:VAL174 3.4 7.2 1.0
C B:ALA169 3.5 6.5 1.0
CD B:GLN195 3.5 9.2 1.0
N B:TYR171 3.7 7.9 1.0
C B:SER170 3.8 8.3 1.0
CA B:SER170 3.9 7.0 1.0
N B:SER176 4.0 6.6 1.0
N B:VAL174 4.1 7.7 1.0
CA B:VAL174 4.1 7.0 1.0
N B:SER170 4.2 6.6 1.0
CA B:TYR171 4.2 7.9 1.0
N B:ASP172 4.2 9.7 1.0
CB B:SER176 4.2 7.0 1.0
CB B:VAL174 4.3 6.9 1.0
CB B:GLN195 4.3 8.3 1.0
CA B:ASP172 4.3 9.3 1.0
O B:SER170 4.3 9.5 1.0
CG B:GLN195 4.4 9.1 1.0
N B:MET175 4.4 6.0 1.0
O B:GLN195 4.4 8.7 1.0
NH1 B:ARG395 4.4 8.6 1.0
C B:ASP172 4.5 9.2 1.0
C B:MET175 4.5 7.8 1.0
NE2 B:GLN195 4.5 9.6 1.0
OE2 B:GLU197 4.6 12.1 1.0
CA B:MET175 4.6 7.4 1.0
O B:ASP172 4.7 10.0 1.0
CA B:ALA169 4.7 6.5 1.0
CA B:SER176 4.7 7.0 1.0
O B:PRO168 4.8 7.4 1.0

Magnesium binding site 6 out of 8 in 1wvm

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Magnesium binding site 6 out of 8 in the Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg612

b:18.4
occ:1.00
 MG B:MG611 2.4 7.8 1.0
O B:GLN195 2.7 8.7 1.0
OE2 B:GLU197 2.7 12.1 1.0
O B:VAL174 2.9 7.9 1.0
N B:SER176 3.0 6.6 1.0
OE1 B:GLN195 3.3 8.5 1.0
CB B:SER176 3.5 7.0 1.0
C B:GLN195 3.7 8.4 1.0
CB B:GLU197 3.7 9.0 1.0
CD B:GLU197 3.9 11.2 1.0
CA B:MET175 3.9 7.4 1.0
O B:ALA169 3.9 7.0 1.0
C B:MET175 3.9 7.8 1.0
CA B:SER176 3.9 7.0 1.0
NH1 B:ARG395 4.0 8.6 1.0
C B:VAL174 4.0 7.2 1.0
CB B:GLN195 4.3 8.3 1.0
CA B:GLN195 4.3 8.8 1.0
CD B:GLN195 4.3 9.2 1.0
CG B:GLU197 4.4 10.1 1.0
N B:MET175 4.4 6.0 1.0
O B:TYR171 4.5 8.9 1.0
N B:GLU197 4.5 8.7 1.0
CA B:GLU197 4.8 8.0 1.0
N B:VAL196 4.8 8.7 1.0
O B:SER176 4.8 6.9 1.0
NH1 B:ARG410 4.8 18.6 1.0
OG B:SER176 4.9 8.0 1.0
C B:VAL196 4.9 7.7 1.0
C B:SER176 4.9 6.3 1.0
OE1 B:GLU197 4.9 13.0 1.0
CG B:GLN195 4.9 9.1 1.0

Magnesium binding site 7 out of 8 in 1wvm

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Magnesium binding site 7 out of 8 in the Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg613

b:14.2
occ:1.00
 O B:HOH772 2.1 17.9 1.0
O B:HOH839 2.1 20.5 1.0
OD1 B:ASN119 3.8 21.1 1.0
O B:HOH788 4.3 15.0 1.0
O B:HOH907 4.4 21.2 1.0
O B:HOH899 4.4 13.6 1.0
O B:HOH782 4.5 15.8 1.0
O B:HOH727 4.8 16.5 1.0
CG B:ASN119 4.9 16.7 1.0
O B:HOH674 5.0 10.4 1.0

Magnesium binding site 8 out of 8 in 1wvm

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Magnesium binding site 8 out of 8 in the Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease APA1 From Antarctic Psychrotroph Pseudoaleromonas Sp. As-11, Complexed with Inhibitor Chymostatin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg614

b:2.2
occ:0.50
 O B:HOH728 2.0 16.9 1.0
O B:HOH676 2.1 14.1 1.0
O B:GLU388 3.9 9.3 1.0
O B:HOH734 4.1 15.1 1.0
O B:PRO387 4.3 9.9 1.0
OE1 B:GLU388 4.3 18.8 1.0
O B:HOH621 4.4 8.0 1.0
C B:GLU388 4.4 9.3 1.0
O B:HOH911 4.4 20.7 1.0
CA B:GLU388 4.5 10.5 1.0
O B:CYS389 4.5 7.5 1.0
CD B:GLU388 4.8 21.8 1.0

Reference:

D.Dong, K.Watanabe. Crystal Structure of Psychrophilic Subtilisin-Like Serine Protease From Antarctic Psychrotroph Pseudoalteromonas Sp. As-11 at 0.16 Nm Resolution To Be Published.
Page generated: Tue Aug 13 17:25:05 2024

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