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Calcium in PDB 3t41: 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (Epip) S393A Mutant From Staphylococcus Aureus

Protein crystallography data

The structure of 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (Epip) S393A Mutant From Staphylococcus Aureus, PDB code: 3t41 was solved by G.Minasov, M.Kuhn, J.Ruan, A.Halavaty, L.Shuvalova, I.Dubrovska, J.Winsor, F.Bagnoli, F.Falugi, M.Bottomley, G.Grandi, W.F.Anderson, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.94 / 1.95
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 71.234, 68.473, 97.723, 90.00, 91.66, 90.00
R / Rfree (%) 16.6 / 19.5

Other elements in 3t41:

The structure of 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (Epip) S393A Mutant From Staphylococcus Aureus also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (Epip) S393A Mutant From Staphylococcus Aureus (pdb code 3t41). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (Epip) S393A Mutant From Staphylococcus Aureus, PDB code: 3t41:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3t41

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Calcium binding site 1 out of 6 in the 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (Epip) S393A Mutant From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (Epip) S393A Mutant From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca458

b:30.2
occ:1.00
 O A:VAL323 2.3 26.2 1.0
O A:HOH502 2.4 29.1 1.0
OD2 A:ASP347 2.4 27.5 1.0
O A:HOH510 2.4 30.8 1.0
O A:HOH474 2.5 29.7 1.0
O A:HOH536 2.5 29.9 1.0
OG1 A:THR325 2.7 26.6 1.0
CG A:ASP347 3.4 28.3 1.0
C A:VAL323 3.5 26.5 1.0
CB A:THR325 3.7 26.4 1.0
OD1 A:ASP347 3.7 29.2 1.0
N A:THR325 3.8 26.7 1.0
O A:TYR345 4.0 30.2 1.0
CA A:VAL323 4.3 29.1 1.0
O A:ALA318 4.3 31.1 1.0
O A:MET320 4.3 33.0 1.0
N A:VAL323 4.3 29.5 1.0
O A:HOH616 4.4 45.2 1.0
CB A:VAL323 4.4 29.3 1.0
CA A:THR325 4.4 24.7 1.0
N A:VAL324 4.4 25.8 1.0
O A:HOH504 4.4 32.5 1.0
CA A:VAL324 4.5 24.1 1.0
C A:VAL324 4.6 25.8 1.0
O B:HOH574 4.6 42.3 1.0
O A:HOH607 4.6 47.5 1.0
O A:HOH648 4.7 59.1 1.0
CB A:ASP347 4.7 26.1 1.0
CG1 A:VAL323 4.9 30.7 1.0
CG2 A:THR325 4.9 25.6 1.0

Calcium binding site 2 out of 6 in 3t41

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Calcium binding site 2 out of 6 in the 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (Epip) S393A Mutant From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (Epip) S393A Mutant From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca459

b:41.9
occ:0.50
 O A:HOH543 2.1 53.7 1.0
O A:HOH686 2.3 53.7 1.0
O A:SER319 2.4 36.7 1.0
O A:HOH616 2.4 45.2 1.0
O A:HOH637 2.7 53.0 1.0
C A:SER319 3.5 35.4 1.0
O A:HOH467 4.0 54.8 1.0
CA A:SER319 4.2 34.9 1.0
O A:ASN344 4.2 36.5 1.0
CB A:SER319 4.3 36.8 1.0
N A:MET320 4.6 34.8 1.0
O A:HOH530 4.6 51.1 1.0
O A:HOH474 4.6 29.7 1.0
C A:MET320 4.7 34.5 1.0
OD1 A:ASP321 4.7 39.8 1.0
CA A:MET320 4.8 34.4 1.0
O A:MET320 4.8 33.0 1.0
OG A:SER319 5.0 40.5 1.0

Calcium binding site 3 out of 6 in 3t41

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Calcium binding site 3 out of 6 in the 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (Epip) S393A Mutant From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (Epip) S393A Mutant From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca460

b:50.2
occ:0.50
 O A:HOH656 2.2 54.3 1.0
O A:LYS280 2.2 40.1 1.0
O A:HOH693 2.2 69.7 1.0
O A:HOH567 2.5 49.1 1.0
O A:HOH655 2.6 57.5 1.0
O A:HOH561 2.6 48.0 1.0
C A:LYS280 3.4 39.5 1.0
O A:HOH694 3.5 81.1 1.0
CB A:LYS280 3.9 41.3 1.0
CA A:LYS280 4.1 40.9 1.0
O A:ALA234 4.4 38.3 1.0
CB A:LYS281 4.4 39.8 1.0
N A:LYS281 4.5 37.8 1.0
O A:HOH471 4.5 68.3 1.0
CA A:GLY237 4.7 39.2 1.0
CA A:LYS281 4.8 37.5 1.0
OG A:SER282 4.8 33.8 1.0
CG A:LYS281 4.9 45.9 1.0
C A:LYS281 4.9 36.3 1.0
O A:LYS281 5.0 35.9 1.0

Calcium binding site 4 out of 6 in 3t41

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Calcium binding site 4 out of 6 in the 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (Epip) S393A Mutant From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (Epip) S393A Mutant From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca458

b:30.0
occ:1.00
 O B:VAL323 2.2 29.1 1.0
O B:HOH511 2.3 27.9 1.0
O B:HOH498 2.4 31.6 1.0
OD2 B:ASP347 2.4 25.2 1.0
O B:HOH464 2.4 31.3 1.0
O B:HOH482 2.5 26.0 1.0
OG1 B:THR325 2.7 26.9 1.0
C B:VAL323 3.4 27.3 1.0
CG B:ASP347 3.4 28.4 1.0
CB B:THR325 3.8 26.8 1.0
OD1 B:ASP347 3.8 27.1 1.0
N B:THR325 3.9 25.8 1.0
O B:TYR345 4.1 28.7 1.0
CA B:VAL323 4.3 28.0 1.0
O B:MET320 4.3 33.7 1.0
O B:ALA318 4.3 30.9 1.0
N B:VAL323 4.3 30.0 1.0
CB B:VAL323 4.4 28.1 1.0
N B:VAL324 4.4 25.8 1.0
O B:HOH496 4.4 34.3 1.0
O B:HOH556 4.4 44.8 1.0
CA B:THR325 4.5 25.4 1.0
CA B:VAL324 4.5 26.6 1.0
C B:VAL324 4.6 26.7 1.0
O B:HOH617 4.6 50.1 1.0
CG1 B:VAL323 4.7 25.2 1.0
O A:HOH618 4.8 52.2 1.0
CB B:ASP347 4.8 26.4 1.0
CG2 B:THR325 5.0 26.1 1.0

Calcium binding site 5 out of 6 in 3t41

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Calcium binding site 5 out of 6 in the 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (Epip) S393A Mutant From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (Epip) S393A Mutant From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca459

b:34.3
occ:0.50
 O B:HOH623 2.1 51.2 1.0
O B:HOH558 2.2 55.4 1.0
O B:HOH691 2.3 35.0 0.5
O B:HOH665 2.4 49.5 1.0
O B:SER319 2.4 34.3 1.0
O B:HOH676 2.4 52.3 1.0
O B:HOH556 2.6 44.8 1.0
C B:SER319 3.6 33.0 1.0
O B:HOH629 4.1 52.8 1.0
O B:HOH655 4.2 63.4 1.0
CA B:SER319 4.3 31.4 1.0
O B:ASN344 4.3 34.1 1.0
CB B:SER319 4.4 33.8 1.0
O B:HOH612 4.4 39.7 1.0
N B:MET320 4.6 31.5 1.0
C B:MET320 4.7 33.0 1.0
OD1 B:ASP321 4.7 44.7 1.0
O B:HOH464 4.7 31.3 1.0
CA B:MET320 4.7 33.1 1.0
O B:MET320 4.8 33.7 1.0
O A:HOH688 4.8 63.2 1.0

Calcium binding site 6 out of 6 in 3t41

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Calcium binding site 6 out of 6 in the 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (Epip) S393A Mutant From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (Epip) S393A Mutant From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca460

b:41.8
occ:0.50
 O B:HOH678 2.2 63.5 1.0
O B:HOH677 2.3 64.7 1.0
O B:HOH605 2.3 49.5 1.0
O B:LYS280 2.3 42.7 1.0
O B:HOH626 2.4 50.2 1.0
O B:HOH579 2.4 51.8 1.0
O B:HOH647 2.5 58.3 1.0
C B:LYS280 3.5 41.9 1.0
CB B:LYS280 4.0 45.0 1.0
CA B:LYS280 4.2 44.0 1.0
O B:ALA234 4.4 43.6 1.0
CB B:LYS281 4.4 41.7 1.0
N B:LYS281 4.6 40.6 1.0
CA B:GLY237 4.8 43.7 1.0
OG B:SER282 4.8 36.5 1.0
CA B:LYS281 4.8 40.1 1.0
C B:LYS281 4.9 38.1 1.0
CE B:LYS280 5.0 58.8 1.0

Reference:

G.Minasov, M.Kuhn, J.Ruan, A.Halavaty, L.Shuvalova, I.Dubrovska, J.Winsor, F.Bagnoli, F.Falugi, M.Bottomley, G.Grandi, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 1.95 Angstrom Resolution Crystal Structure of Epidermin Leader Peptide Processing Serine Protease (Epip) S393A Mutant From Staphylococcus Aureus. To Be Published.
Page generated: Tue Jul 8 16:49:04 2025

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